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- PDB-4c1c: Crystal structure of the metallo-beta-lactamase BCII with D-captopril -

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Basic information

Entry
Database: PDB / ID: 4c1c
TitleCrystal structure of the metallo-beta-lactamase BCII with D-captopril
ComponentsBETA-LACTAMASE 2
KeywordsHYDROLASE / MBL. METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
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-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...: / 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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MCO / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6247
Polymers24,9961
Non-polymers6286
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.160, 61.530, 69.520
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2102-

HOH

21A-2198-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA-LACTAMASE 2 / BETA-LACTAMASE II / CEPHALOSPORINASE / PENICILLINASE / BCII


Mass: 24995.533 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: 569/H/9 / Description: CHROMOSOME DERIVED. / Plasmid: PET-9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P04190, beta-lactamase

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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 growpH: 5.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M BIS TRIS, 25 % W/V PEG 3350, PH 5.5, 1 MM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.18→40.19 Å / Num. obs: 69596 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 1.18→1.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 90.4

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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 1MQO

1mqo


Resolution: 1.18→40.195 Å / SU ML: 0.11 / σ(F): 0.78 / Phase error: 12.4 / Stereochemistry target values: ML
Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 86 ASP, 87 SER AND 245 ASP VALIDATED BY CLEAR ELECTRON DENSITY. RAMACHANDRAN OUTLIER 117 ALA VALIDATED BY ELECTRON DENSITY AND IS CONSISTENT WITH ...Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 86 ASP, 87 SER AND 245 ASP VALIDATED BY CLEAR ELECTRON DENSITY. RAMACHANDRAN OUTLIER 117 ALA VALIDATED BY ELECTRON DENSITY AND IS CONSISTENT WITH CONFORMATION IN PDB ENTRY 4C09. POSSIBLE OXIDISED CYS 198 AT VERY LOW OCCUPANCY LEFT UNMODELED DUE TO LOW OCCUPANCY. RESIDUES 41-44 AND 63-67 ARE DISORDERED WITH 64-66 UNMODELED.
RfactorNum. reflection% reflection
Rfree0.1355 1997 2.9 %
Rwork0.12 --
obs0.1204 69587 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.33 Å2
Refinement stepCycle: LAST / Resolution: 1.18→40.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 33 266 1961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011837
X-RAY DIFFRACTIONf_angle_d1.4272510
X-RAY DIFFRACTIONf_dihedral_angle_d13.843666
X-RAY DIFFRACTIONf_chiral_restr0.086294
X-RAY DIFFRACTIONf_plane_restr0.007323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.20950.24311310.20494565X-RAY DIFFRACTION90
1.2095-1.24220.20791360.17614629X-RAY DIFFRACTION91
1.2422-1.27880.20711460.15744701X-RAY DIFFRACTION93
1.2788-1.32010.16491460.12894679X-RAY DIFFRACTION93
1.3201-1.36720.15691290.11394790X-RAY DIFFRACTION94
1.3672-1.4220.13571450.09914763X-RAY DIFFRACTION94
1.422-1.48670.10941350.09554806X-RAY DIFFRACTION95
1.4867-1.56510.09461480.08834846X-RAY DIFFRACTION95
1.5651-1.66320.11881430.08224848X-RAY DIFFRACTION96
1.6632-1.79160.10991410.08874889X-RAY DIFFRACTION96
1.7916-1.97190.1011510.09464938X-RAY DIFFRACTION97
1.9719-2.25720.11911500.10614979X-RAY DIFFRACTION97
2.2572-2.84370.1281440.13095029X-RAY DIFFRACTION98
2.8437-40.21820.15611520.13825128X-RAY DIFFRACTION99

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