[English] 日本語
Yorodumi
- PDB-2gkl: Crystal structure of the zinc carbapenemase CPHA in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gkl
TitleCrystal structure of the zinc carbapenemase CPHA in complex with the inhibitor pyridine-2,4-dicarboxylate
ComponentsBeta-lactamase
KeywordsHYDROLASE / LACTAMASE / INHIBITOR / ZN
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 / 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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDINE-2,4-DICARBOXYLIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGarau, G. / Dideberg, O.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2007
Title: Competitive Inhibitors of the CphA Metallo-{beta}-Lactamase from Aeromonas hydrophila
Authors: Horsfall, L.E. / Garau, G. / Lienard, B.M.R. / Dideberg, O. / Schofield, C.J. / Frere, J.M. / Galleni, M.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem
Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O.
#2: Journal: Antimicrob.Agents Chemother. / Year: 2004
Title: Update of the standard numbering scheme for class B beta-lactamases
Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.M. / Dideberg, O.
#3: Journal: Embo J. / Year: 1995
Title: The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / pdbx_struct_special_symmetry / 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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7306
Polymers25,2211
Non-polymers5095
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.638, 101.211, 117.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

-
Components

#1: Protein Beta-lactamase


Mass: 25220.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: PUC20-CPHA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P26918, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS COORDINATES USE NON-SEQUENTIAL RESIDUE NUMBERING. THE NUMBERING RELATES TO PDB ENTRY 1X8H.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 21756 / Num. obs: 21647 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 6 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.179 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.2.0019refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8H

1x8h


Resolution: 1.86→21.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.188 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19617 1102 5.1 %RANDOM
Rwork0.15898 ---
all0.161 21625 --
obs0.16084 20495 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.86→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 31 190 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221835
X-RAY DIFFRACTIONr_bond_other_d0.0070.021239
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9742476
X-RAY DIFFRACTIONr_angle_other_deg1.2183.0013021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92223.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.365159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_nbd_refined0.3590.2439
X-RAY DIFFRACTIONr_nbd_other0.2050.21340
X-RAY DIFFRACTIONr_nbtor_refined0.180.2888
X-RAY DIFFRACTIONr_nbtor_other0.0880.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.228
X-RAY DIFFRACTIONr_mcbond_it0.7581.51130
X-RAY DIFFRACTIONr_mcbond_other0.2051.5451
X-RAY DIFFRACTIONr_mcangle_it1.18121784
X-RAY DIFFRACTIONr_scbond_it2.1853800
X-RAY DIFFRACTIONr_scangle_it3.4744.5692
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 77 -
Rwork0.162 1425 -
obs--95.24 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more