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- PDB-6lf4: Crystal structure of VMB-1 bound to hydrolyzed meropenem -

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Basic information

Entry
Database: PDB / ID: 6lf4
TitleCrystal structure of VMB-1 bound to hydrolyzed meropenem
ComponentsVMB-1 metallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase / subclasse B1
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LMP / beta-lactamase
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsCheng, Q. / Chen, S.
CitationJournal: To Be Published
Title: Crystal structure of VMB-1 bound to hydrolyzed meropenem
Authors: Chen, S. / Cheng, Q.
History
DepositionNov 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / software / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VMB-1 metallo-beta-lactamase
B: VMB-1 metallo-beta-lactamase
C: VMB-1 metallo-beta-lactamase
D: VMB-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,95016
Polymers102,8214
Non-polymers2,12912
Water4,900272
1
A: VMB-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2374
Polymers25,7051
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VMB-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2374
Polymers25,7051
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: VMB-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2374
Polymers25,7051
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: VMB-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2374
Polymers25,7051
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.108, 96.777, 131.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
VMB-1 metallo-beta-lactamase


Mass: 25705.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5Q5ADH9*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LMP / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Meropenem


Mass: 401.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350
PH range: 5.4-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979191 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.008→77.99 Å / Num. obs: 63155 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 32.08 Å2 / CC1/2: 0.92 / Net I/σ(I): 4.8
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9088 / CC1/2: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JV4

6jv4


Resolution: 2.01→77.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.369 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 3136 5 %RANDOM
Rwork0.2094 ---
obs0.2118 59946 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 35.999 Å2 / Biso min: 19.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-0 Å2
2---0.65 Å20 Å2
3---2.88 Å2
Refinement stepCycle: final / Resolution: 2.01→77.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 0 116 272 7156
Biso mean--65.78 39.26 -
Num. residues----876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176596
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6569584
X-RAY DIFFRACTIONr_angle_other_deg1.3361.59915384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93425.493284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.399151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.082158
X-RAY DIFFRACTIONr_chiral_restr0.2560.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
LS refinement shellResolution: 2.01→2.06 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.262 232 -
Rwork0.245 4375 -
obs--99.78 %

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