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- PDB-4c1e: Crystal structure of the metallo-beta-lactamase VIM-2 with D-captopril -

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Basic information

Entry
Database: PDB / ID: 4c1e
TitleCrystal structure of the metallo-beta-lactamase VIM-2 with D-captopril
ComponentsBETA-LACTAMASE CLASS B VIM-2
KeywordsHYDROLASE / MBL. METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / 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-MCO / beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsZollman, D. / Brem, J. / McDonough, M.A. / van Berkel, S.S. / Schofield, C.J.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers.
Authors: Brem, J. / van Berkel, S.S. / Zollman, D. / Lee, S.Y. / Gileadi, O. / McHugh, P.J. / Walsh, T.R. / McDonough, M.A. / Schofield, C.J.
History
DepositionAug 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Other / Structure summary
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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 CLASS B VIM-2
B: BETA-LACTAMASE CLASS B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,49017
Polymers51,3872
Non-polymers1,10315
Water9,620534
1
A: BETA-LACTAMASE CLASS B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2689
Polymers25,6931
Non-polymers5758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE CLASS B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2228
Polymers25,6931
Non-polymers5297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.921, 79.034, 67.229
Angle α, β, γ (deg.)90.00, 131.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE CLASS B VIM-2 / CLASS B BETA-LACTAMASE / METALLO BETA LACTAMASE VIM-2 / METALLO BETA-LACTAMASE / METALLO-BETA- ...CLASS B BETA-LACTAMASE / METALLO BETA LACTAMASE VIM-2 / METALLO BETA-LACTAMASE / METALLO-BETA-LACTAMASE / METALLO-BETA-LACTAMASE VIM-2 / METTALO-BETA-LACTAMASE VIM-2 / VIM-2 / VIM-2 PROTEIN / VIM-2 TYPE METALLO-BETA-LACTAMASE


Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Description: PLASMID DERIVED NON-GENOMIC. / Plasmid: OPINF VECTOR BASED ON PTRIEX VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9K2N0, beta-lactamase

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Non-polymers , 5 types, 549 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15NO3S
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details((S)-3-MERCAPTO-2-METHYLPROPANOYL)-D-PROLINE (MCO): D-CAPTOPRIL

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Oct 17, 2012 / Details: VARIMAX HF
RadiationMonochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 78943 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 13.46 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3


Resolution: 1.399→31.21 Å / SU ML: 0.13 / σ(F): 1.33 / Phase error: 17 / Stereochemistry target values: ML
Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 84 ASP, 87 TRP AND 178 ALA VALIDATED BY CLEAR ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.1672 1648 2.1 %
Rwork0.1317 --
obs0.1324 78862 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.89 Å2
Refinement stepCycle: LAST / Resolution: 1.399→31.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 51 534 4069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0243834
X-RAY DIFFRACTIONf_angle_d1.425287
X-RAY DIFFRACTIONf_dihedral_angle_d13.131357
X-RAY DIFFRACTIONf_chiral_restr0.083591
X-RAY DIFFRACTIONf_plane_restr0.008701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3988-1.440.22761270.18626114X-RAY DIFFRACTION94
1.44-1.48650.20231420.16836303X-RAY DIFFRACTION97
1.4865-1.53960.24511300.15286419X-RAY DIFFRACTION99
1.5396-1.60120.17571390.13756434X-RAY DIFFRACTION99
1.6012-1.67410.20051330.13356470X-RAY DIFFRACTION99
1.6741-1.76240.20381390.12096382X-RAY DIFFRACTION98
1.7624-1.87280.1331330.11976350X-RAY DIFFRACTION98
1.8728-2.01730.16941460.11836505X-RAY DIFFRACTION100
2.0173-2.22030.15191380.11096534X-RAY DIFFRACTION100
2.2203-2.54140.17471440.12416515X-RAY DIFFRACTION100
2.5414-3.20140.16251320.13676555X-RAY DIFFRACTION100
3.2014-31.21760.14981450.13466633X-RAY DIFFRACTION100

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