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- PDB-5fqc: Crystal structure of the metallo-beta-lactamase VIM-2 with 2C -

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Basic information

Entry
Database: PDB / ID: 5fqc
TitleCrystal structure of the metallo-beta-lactamase VIM-2 with 2C
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / : / 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
FORMIC ACID / Chem-OK3 / beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsBrem, J. / Cain, R. / McDonough, M.A. / Clifton, I.J. / Fishwick, C.W.G. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.
Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J.
History
DepositionDec 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.0Oct 30, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / exptl_crystal_grow / pdbx_database_status / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Revision 2.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,75615
Polymers51,3872
Non-polymers1,36913
Water8,053447
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4178
Polymers25,6931
Non-polymers7247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3397
Polymers25,6931
Non-polymers6456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.931, 79.152, 67.135
Angle α, β, γ (deg.)90.00, 130.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2006-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0989, -0.0067, 0.9951), (0.073, -0.9972, -0.014), (0.9924, 0.0741, -0.0981)
Vector: -90.3705, -0.6144, 99.2331)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE / BETA-LACTAMASE VIM-2


Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-266
Source method: isolated from a genetically manipulated source
Details: 2C BOUND TO THE ACTIVE SITE / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: OPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, beta-lactamase

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Non-polymers , 5 types, 460 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OK3 / (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid


Mass: 357.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18BN2O6
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCLEAVED N-TERMINAL HISTAG

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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: 1.73 Å3/Da / Density % sol: 28.9 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→28.89 Å / Num. obs: 71728 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 14.52 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BZ3

4bz3


Resolution: 1.449→28.886 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 1975 2.8 %
Rwork0.1547 --
obs0.1555 71728 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.449→28.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 74 447 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143733
X-RAY DIFFRACTIONf_angle_d1.415128
X-RAY DIFFRACTIONf_dihedral_angle_d13.9271304
X-RAY DIFFRACTIONf_chiral_restr0.094576
X-RAY DIFFRACTIONf_plane_restr0.01678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4492-1.48540.26121340.25114867X-RAY DIFFRACTION97
1.4854-1.52560.26881370.22645007X-RAY DIFFRACTION100
1.5256-1.57050.27481420.21574965X-RAY DIFFRACTION100
1.5705-1.62110.21451420.20725002X-RAY DIFFRACTION100
1.6211-1.67910.23371430.19095006X-RAY DIFFRACTION100
1.6791-1.74630.21821400.17024969X-RAY DIFFRACTION100
1.7463-1.82580.16551430.15655010X-RAY DIFFRACTION100
1.8258-1.9220.17991480.15165009X-RAY DIFFRACTION100
1.922-2.04240.16821360.14365003X-RAY DIFFRACTION100
2.0424-2.20.16531470.13884976X-RAY DIFFRACTION100
2.2-2.42130.18051430.14635003X-RAY DIFFRACTION100
2.4213-2.77150.19781420.14624992X-RAY DIFFRACTION99
2.7715-3.49080.18481400.14134944X-RAY DIFFRACTION98
3.4908-28.89160.15341380.14234992X-RAY DIFFRACTION97

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