[English] 日本語
Yorodumi
- PDB-1x8h: The Mono-Zinc Carbapenemase CphA (N220G mutant) Shows a Zn(II)- N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x8h
TitleThe Mono-Zinc Carbapenemase CphA (N220G mutant) Shows a Zn(II)- NH2 ARG Coordination
ComponentsBeta-lactamase
KeywordsHYDROLASE
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 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
CARBONATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsGarau, G. / Dideberg, O.
Citation
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.
#1: 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.
#2: 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.
#3: Journal: J.Am.Chem.Soc. / Year: 2002
Title: Guanidine is a Zn(2+)-binding ligand at neutral pH in aqueous solution
Authors: Aoki, S. / Iwaida, K. / Hanamoto, N. / Shiro, M. / Kimura, E.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 17, 2016Group: Derived calculations
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8498
Polymers25,2511
Non-polymers5987
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.683, 101.286, 117.820
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-3-

SO4

21A-473-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 25250.846 Da / Num. of mol.: 1 / Mutation: N220G
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

-
Non-polymers , 5 types, 265 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 18, 2003
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 32222 / % possible obs: 93.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 8.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 8.1 / Rsym value: 0.07 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.204 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17957 1598 5 %RANDOM
Rwork0.15259 ---
all0.153 ---
obs0.15397 30092 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 32 258 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221863
X-RAY DIFFRACTIONr_bond_other_d0.0020.021682
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9742511
X-RAY DIFFRACTIONr_angle_other_deg1.04233931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021971
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02360
X-RAY DIFFRACTIONr_nbd_refined0.4130.2420
X-RAY DIFFRACTIONr_nbd_other0.2430.21907
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.2982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7351.51129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29921810
X-RAY DIFFRACTIONr_scbond_it2.0763734
X-RAY DIFFRACTIONr_scangle_it3.3574.5701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free8.37922
X-RAY DIFFRACTIONr_sphericity_bonded4.17328
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.186 97
Rwork0.14 1770

+
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