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- PDB-6jv4: Crystal structure of metallo-beta-lactamase VMB-1 -

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Basic information

Entry
Database: PDB / ID: 6jv4
TitleCrystal structure of metallo-beta-lactamase VMB-1
ComponentsVMB-1
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
CITRIC ACID / beta-lactamase
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCheng, Q. / Chen, S.
CitationJournal: Adv Biosyst / Year: 2020
Title: Genetic and Biochemical Characterization of VMB-1, a Novel Metallo-beta-Lactamase Encoded by a Conjugative, Broad-Host Range IncC Plasmid from Vibrio spp.
Authors: Zheng, Z. / Cheng, Q. / Chan, E.W. / Chen, S.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,11216
Polymers102,8214
Non-polymers1,29212
Water8,971498
1
A: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0284
Polymers25,7051
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-79 kcal/mol
Surface area9980 Å2
MethodPISA
2
B: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0284
Polymers25,7051
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-78 kcal/mol
Surface area9870 Å2
MethodPISA
3
C: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0284
Polymers25,7051
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-77 kcal/mol
Surface area9920 Å2
MethodPISA
4
D: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0284
Polymers25,7051
Non-polymers3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-79 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.957, 94.981, 145.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
VMB-1 / Metallo-beta-lactamases


Mass: 25705.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: vmb-1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5Q5ADH9
#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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 1.8 M Ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 143862 / % possible obs: 99.2 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 17
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 12 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.625 / Num. unique obs: 14078 / Rsym value: 1.31 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.56 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18928 7331 5.1 %RANDOM
Rwork0.16656 ---
obs0.16771 136108 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.09 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.7→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6810 0 60 498 7368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0137043
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176549
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6339544
X-RAY DIFFRACTIONr_angle_other_deg1.5051.57815272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63825.524286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.856151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.14158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021279
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4911.4393524
X-RAY DIFFRACTIONr_mcbond_other1.4781.4383523
X-RAY DIFFRACTIONr_mcangle_it2.2142.1484398
X-RAY DIFFRACTIONr_mcangle_other2.2142.1494399
X-RAY DIFFRACTIONr_scbond_it2.7981.7533519
X-RAY DIFFRACTIONr_scbond_other2.7891.7523516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2312.485147
X-RAY DIFFRACTIONr_long_range_B_refined5.02317.4467700
X-RAY DIFFRACTIONr_long_range_B_other4.96617.2327612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.248 510 -
Rwork0.234 9654 -
obs--96.06 %

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