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- PDB-4c1g: Crystal structure of the metallo-beta-lactamase IMP-1 with D-captopril -

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Basic information

Entry
Database: PDB / ID: 4c1g
TitleCrystal structure of the metallo-beta-lactamase IMP-1 with D-captopril
ComponentsBETA-LACTAMASE IMP-1
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / 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-lactamases class B signature 1. / 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 ...Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / 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-MCO / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.714 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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_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 IMP-1
B: BETA-LACTAMASE IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9649
Polymers50,2932
Non-polymers6717
Water3,873215
1
A: BETA-LACTAMASE IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6876
Polymers25,1471
Non-polymers5405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2773
Polymers25,1471
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 54.570, 194.590
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 BETA-LACTAMASE IMP-1 / BLAIMP / BETA-LACTAMASE TYPE II / PENICILLINASE


Mass: 25146.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Description: PLASMID DERIVED NON-GENOMIC. / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P52699, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
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 growpH: 4.5
Details: 0.05 M LI2SO4, 0.1 M SODIUM ACETATE, PH 4.5, 23 % W/V PEG 8000, 1MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.71→64.86 Å / Num. obs: 58579 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 1.71→1.76 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DD6

1dd6


Resolution: 1.714→52.543 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 15.69 / Stereochemistry target values: ML
Details: CHAIN B MUCH MORE DISORDERED THAN CHAIN A SO INHIBITOR ONLY SEEN IN A. CONFORMATION OF RAMACHANDRAN OUTLIERS 59 ASN AND 66 ASP VALIDATED BY CLEAR ELECTRON DENSITY IN CHAIN A.
RfactorNum. reflection% reflection
Rfree0.1758 3846 3.5 %
Rwork0.145 --
obs0.1461 58470 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.19 Å2
Refinement stepCycle: LAST / Resolution: 1.714→52.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 28 215 3495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023414
X-RAY DIFFRACTIONf_angle_d1.734673
X-RAY DIFFRACTIONf_dihedral_angle_d13.6051156
X-RAY DIFFRACTIONf_chiral_restr0.111526
X-RAY DIFFRACTIONf_plane_restr0.01589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7139-1.73560.30911500.23313993X-RAY DIFFRACTION100
1.7356-1.75850.26311540.21873921X-RAY DIFFRACTION100
1.7585-1.78250.24461430.20083920X-RAY DIFFRACTION100
1.7825-1.8080.20971220.18014016X-RAY DIFFRACTION100
1.808-1.8350.23891220.16763945X-RAY DIFFRACTION100
1.835-1.86370.18671530.15443993X-RAY DIFFRACTION100
1.8637-1.89420.1831500.15013939X-RAY DIFFRACTION100
1.8942-1.92690.19961640.13983957X-RAY DIFFRACTION100
1.9269-1.96190.15671390.12973964X-RAY DIFFRACTION100
1.9619-1.99970.15111280.12783999X-RAY DIFFRACTION100
1.9997-2.04050.18091500.12793949X-RAY DIFFRACTION100
2.0405-2.08490.19451540.13293942X-RAY DIFFRACTION100
2.0849-2.13340.1431550.12713929X-RAY DIFFRACTION100
2.1334-2.18670.15081450.11654015X-RAY DIFFRACTION100
2.1867-2.24580.14981360.11873898X-RAY DIFFRACTION100
2.2458-2.31190.15461290.11784003X-RAY DIFFRACTION100
2.3119-2.38650.13621410.11863987X-RAY DIFFRACTION100
2.3865-2.47180.16721450.12473961X-RAY DIFFRACTION100
2.4718-2.57080.15191440.12563942X-RAY DIFFRACTION100
2.5708-2.68780.15521320.12753920X-RAY DIFFRACTION100
2.6878-2.82950.18221540.14163965X-RAY DIFFRACTION100
2.8295-3.00680.1751340.14223999X-RAY DIFFRACTION100
3.0068-3.23890.15971520.14463946X-RAY DIFFRACTION100
3.2389-3.56480.21351310.14553978X-RAY DIFFRACTION100
3.5648-4.08040.17991440.14593949X-RAY DIFFRACTION100
4.0804-5.14020.171350.14083939X-RAY DIFFRACTION100
5.1402-52.56770.17781400.19343976X-RAY DIFFRACTION100

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