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- PDB-4c1f: Crystal structure of the metallo-beta-lactamase IMP-1 with L-captopril -

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Basic information

Entry
Database: PDB / ID: 4c1f
TitleCrystal structure of the metallo-beta-lactamase IMP-1 with L-captopril
ComponentsBETA-LACTAMASE IMP-1
KeywordsHYDROLASE / MBL / METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-CAPTOPRIL / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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

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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)51,06010
Polymers50,2932
Non-polymers7678
Water2,882160
1
A: BETA-LACTAMASE IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7837
Polymers25,1471
Non-polymers6366
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)193.620, 49.910, 54.620
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 / IMP-1 / BLAIMP / BETA-LACTAMASE TYPE II / PENICILLINASE


Mass: 25146.676 Da / Num. of mol.: 2 / Fragment: RESIDUES 19-245
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-X8Z / L-CAPTOPRIL


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Comment: inhibitor, medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: I03 / Wavelength: 0.9626
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9626 Å / Relative weight: 1
ReflectionResolution: 2.01→52.5 Å / Num. obs: 36158 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 27.43 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 99.1

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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 1DD6

1dd6


Resolution: 2.01→52.568 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 21.05 / Stereochemistry target values: ML
Details: CHAIN B IS MORE DISORDERED THAN CHAIN A AS INDICATED BY THE AVERAGE B-FACTORS - CHAIN A 22.3 VS CHAIN B 70.7. CONFORMATION OF RAMACHANDRAN OUTLIERS 59 ASN AND 66 ASP VALIDATED BY CLEAR ...Details: CHAIN B IS MORE DISORDERED THAN CHAIN A AS INDICATED BY THE AVERAGE B-FACTORS - CHAIN A 22.3 VS CHAIN B 70.7. CONFORMATION OF RAMACHANDRAN OUTLIERS 59 ASN AND 66 ASP VALIDATED BY CLEAR ELECTRON DENSITY IN CHAIN A.
RfactorNum. reflection% reflection
Rfree0.2244 1805 5 %
Rwork0.1839 --
obs0.186 36155 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 2.01→52.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 33 160 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043459
X-RAY DIFFRACTIONf_angle_d0.7664717
X-RAY DIFFRACTIONf_dihedral_angle_d12.6551194
X-RAY DIFFRACTIONf_chiral_restr0.043527
X-RAY DIFFRACTIONf_plane_restr0.003591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.06440.22611380.16982594X-RAY DIFFRACTION100
2.0644-2.12510.20591360.17532574X-RAY DIFFRACTION100
2.1251-2.19370.26631410.192622X-RAY DIFFRACTION100
2.1937-2.27210.27531250.19282628X-RAY DIFFRACTION100
2.2721-2.36310.25821100.19062609X-RAY DIFFRACTION100
2.3631-2.47060.24531390.2022633X-RAY DIFFRACTION100
2.4706-2.60090.2361280.19012619X-RAY DIFFRACTION100
2.6009-2.76380.23961460.19252616X-RAY DIFFRACTION100
2.7638-2.97720.2281490.1892608X-RAY DIFFRACTION100
2.9772-3.27680.18881380.18352653X-RAY DIFFRACTION100
3.2768-3.75080.21911530.16732659X-RAY DIFFRACTION100
3.7508-4.72510.21041460.16482694X-RAY DIFFRACTION100
4.7251-52.58630.22411560.20062841X-RAY DIFFRACTION99

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