BMRB Entry 19048

Name: Solution Structure of the Bacillus cereus Metallo-Beta-Lactamase BcII in Complex with R-Thiomandelic Acid
Published: 2013-08-14

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PDB ID: 2m5d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19048
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution Structure of the Bacillus cereus Metallo-Beta-Lactamase BcII in Complex with R-Thiomandelic Acid PubMed: 23838816

Deposition date: 2013-02-20 Original release date: 2013-08-14

Authors: Karsisiotis, Andreas Ioannis; Damblon, Christian; Roberts, Gordon

Citation: Karsisiotis, Andreas Ioannis; Damblon, Christian; Roberts, Gordon. "Complete 1H, 15N and 13C resonance assignments of Bacillus cereus metallo-beta-lactamase and its complex with the inhibitor R-thiomandelic acid" Biomol. NMR Assign. ., .-. (2013).

Assembly members:
BcII, polymer, 227 residues, 24995.738 Da.
3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide, non-polymer, 311.421 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source: Common Name: Firmicutes Taxonomy ID: 1396 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacillus cereus

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
BcII: SQKVEKTVIKNETGTISISQ LNKNVWVHTELGSFNGEAVP SNGLVLNTSKGLVLVDSSWD DKLTKELIEMVEKKFQKRVT DVIITHAHADRIGGIKTLKE RGIKAHSTALTAELAKKNGY EEPLGDLQTVTNLKFGNMKV ETFYPGKGHTEDNIVVWLPQ YNILVGGCLVKSTSAKDLGN VADAYVNEWSTSIENVLKRY RNINAVVPGHGEVGDKGLLL HTLDLLK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	730
15N chemical shifts	231
1H chemical shifts	3080

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	BcII	1
2	RTM	2
3	ZINC ION_1	3
4	ZINC ION_2	3

Entities:

Entity 1, BcII 227 residues - 24995.738 Da.

1

SER

GLN

LYS

VAL

GLU

LYS

THR

VAL

ILE

LYS

2

ASN

GLU

THR

GLY

THR

ILE

SER

ILE

SER

GLN

3

LEU

ASN

LYS

ASN

VAL

TRP

VAL

HIS

THR

GLU

4

LEU

GLY

SER

PHE

ASN

GLY

GLU

ALA

VAL

PRO

5

SER

ASN

GLY

LEU

VAL

LEU

ASN

THR

SER

LYS

6

GLY

LEU

VAL

LEU

VAL

ASP

SER

TRP

ASP

7

ASP

LYS

LEU

THR

LYS

GLU

LEU

ILE

GLU

MET

8

VAL

GLU

LYS

PHE

GLN

LYS

ARG

VAL

THR

9

ASP

VAL

ILE

THR

HIS

ALA

HIS

ALA

ASP

10

ARG

ILE

GLY

ILE

LYS

THR

LEU

LYS

GLU

11

ARG

GLY

ILE

LYS

ALA

HIS

SER

THR

ALA

LEU

12

THR

ALA

GLU

LEU

ALA

LYS

ASN

GLY

TYR

13

GLU

PRO

LEU

GLY

ASP

LEU

GLN

THR

VAL

14

THR

ASN

LEU

LYS

PHE

GLY

ASN

MET

LYS

VAL

15

GLU

THR

PHE

TYR

PRO

GLY

LYS

GLY

HIS

THR

16

GLU

ASP

ASN

ILE

VAL

TRP

LEU

PRO

GLN

17

TYR

ASN

ILE

LEU

VAL

GLY

CYS

LEU

VAL

18

LYS

SER

THR

SER

ALA

LYS

ASP

LEU

GLY

ASN

19

VAL

ALA

ASP

ALA

TYR

VAL

ASN

GLU

TRP

SER

20

THR

SER

ILE

GLU

ASN

VAL

LEU

LYS

ARG

TYR

21

ARG

ASN

ILE

ASN

ALA

VAL

PRO

GLY

HIS

22

GLY

GLU

VAL

GLY

ASP

LYS

GLY

LEU

23

HIS

THR

LEU

ASP

LEU

LYS

Entity 2, RTM - C19 H25 N3 O - 311.421 Da.

1

RTM

Entity 3, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: BcII, [U-99% 15N], 1 mM; R-Thiomandelic Acid 1 mM; MES 20 mM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_2: BcII, [U-99% 13C; U-99% 15N], 1 mM; R-Thiomandelic Acid 1 mM; MES 20 mM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 6.4; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

CANDID, Guntert, Mumenthaler and Wuthrich - automated NOE assignment, structure solution

SPARKY, Goddard - data analysis, peak picking

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN, Bruker Biospin - collection

xwinnmr, Bruker Biospin - collection

ProcheckNMR, Laskowski and MacArthur - validation

WhatIF, Vriend - validation

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz
Bruker Avance 600 MHz

GB	M11189 AAA22276 AGE79265 AHX19465 AHZ52262 AIA18213
GenPept	AAA22276
BMRB	19047
PDB	1BC2 1BMC 1BVT 1DXK 1MQO 2BC2 2BFK 2BFL 2BFZ 2BG2 2BG6 2BG7 2BG8 2BGA 2M5C 2M5D 2NXA 2NYP 2NZE 2NZF 2UYX 3BC2 3FCZ 3I11 3I13 3I15 3KNR 3KNS 4C09 4C1C 4C1H 4NQ4 4NQ5 4NQ6 4NQ7 4TYT
EMBL	CGG57718 COF89432 COP86624 COR95834 CRG01336
REF	WP_000742467 WP_000742468 WP_000742469 WP_000742470 WP_000742471
SP	P04190

Biological Magnetic Resonance Data Bank