[English] 日本語
Yorodumi
- PDB-1m2x: Crystal Structure of the metallo-beta-lactamase BlaB of Chryseoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m2x
TitleCrystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum in complex with the inhibitor D-captopril
Componentsclass B carbapenemase BlaB-1
KeywordsHYDROLASE / ALPHA-BETA/BETA-ALPHA FOLD.
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
Chem-MCO / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGarcia-Saez, I. / Dideberg, O.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The 1.5 A structure of Chryseobacterium meningosepticum Zn-beta-lactamase in complex with the inhibitor, D-captopril
Authors: Garcia-Saez, I. / Hopkins, J. / Papamicael, C. / Franceschini, N. / Amicosante, G. / Rossolini, G.M. / Galleni, M. / Frere, J.M. / Dideberg, O.
History
DepositionJun 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / 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_asym_id / _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_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_asym_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_asym_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: class B carbapenemase BlaB-1
B: class B carbapenemase BlaB-1
C: class B carbapenemase BlaB-1
D: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53525
Polymers101,4904
Non-polymers2,04521
Water12,953719
1
A: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9017
Polymers25,3731
Non-polymers5296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8786
Polymers25,3731
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8786
Polymers25,3731
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8786
Polymers25,3731
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.685, 159.685, 97.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
class B carbapenemase BlaB-1 / metallo-beta-lactamase BlaB


Mass: 25372.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: blaB / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: O08498, beta-lactamase

-
Non-polymers , 5 types, 740 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15NO3S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 28% PEG 4K, 0.2M Na Acetate, 0.1M Tris/Hcl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMsodium cacodylate1drop
3100000 mMzinc acetate1drop
4100000 mMdithiothreitol1droppH6.5
528 %PEG40001reservoir
60.2 Msodium acetate1reservoir
70.1 MTris-HCl1reservoirpH8.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 138708 / Num. obs: 138708 / % possible obs: 90 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 13.189 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.117 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.2 / Num. unique all: 15550 / Rsym value: 0.177 / % possible all: 91.8
Reflection
*PLUS
Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.18

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BVT

1bvt


Resolution: 1.5→10 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal showed cubic pseudo-symmetry. It belongs to the space group R3. NCS operators were not used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 12032 -random
Rwork0.19 ---
obs-133860 90 %-
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7034 0 93 719 7846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.5-1.510.2352520.2151X-RAY DIFFRACTION25254
1.97-20.21512400.1887X-RAY DIFFRACTION24034
2.41-2.480.19252380.1878X-RAY DIFFRACTION24564
4.39-5.530.20762150.1753X-RAY DIFFRACTION22734
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.005

+
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