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- PDB-6lfd: Crystal structure of VMB-1 at pH5.5(Bis-Tris) -

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Basic information

Entry
Database: PDB / ID: 6lfd
TitleCrystal structure of VMB-1 at pH5.5(Bis-Tris)
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsCheng, Q. / Chen, S.
CitationJournal: To Be Published
Title: Crystal structure of VMB-1 at pH 5.5(Bis-Tris)
Authors: Chen, S. / Cheng, Q.
History
DepositionDec 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)103,52814
Polymers102,8214
Non-polymers70710
Water7,368409
1
A: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8363
Polymers25,7051
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0205
Polymers25,7051
Non-polymers3154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8363
Polymers25,7051
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: VMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8363
Polymers25,7051
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.110, 97.110, 132.660
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-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 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: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.92→38.69 Å / Num. obs: 72855 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.913 / Net I/σ(I): 4.2
Reflection shellResolution: 1.92→1.97 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5313 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JV4

6jv4


Resolution: 1.92→38.69 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.202 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 3709 5.1 %RANDOM
Rwork0.2003 ---
obs0.2023 69071 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.07 Å2 / Biso mean: 31.774 Å2 / Biso min: 17.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-0 Å2
2---0.7 Å20 Å2
3---1.78 Å2
Refinement stepCycle: final / Resolution: 1.92→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 20 409 7203
Biso mean--33.51 38.63 -
Num. residues----877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136960
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176516
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6339438
X-RAY DIFFRACTIONr_angle_other_deg1.3081.57815194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1625.493284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.823151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.279158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 281 -
Rwork0.22 5020 -
all-5301 -
obs--100 %

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