[English] 日本語
Yorodumi
- PDB-1bue: NMC-A CARBAPENEMASE FROM ENTEROBACTER CLOACAE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bue
TitleNMC-A CARBAPENEMASE FROM ENTEROBACTER CLOACAE
ComponentsPROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE)
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / CLASS A CARBAPENEMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Imipenem-hydrolyzing beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.64 Å
AuthorsSwaren, P. / Maveyraud, L. / Cabantous, S. / Pedelacq, J.D. / Mourey, L. / Frere, J.M. / Samama, J.P.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: X-ray analysis of the NMC-A beta-lactamase at 1.64-A resolution, a class A carbapenemase with broad substrate specificity.
Authors: Swaren, P. / Maveyraud, L. / Raquet, X. / Cabantous, S. / Duez, C. / Pedelacq, J.D. / Mariotte-Boyer, S. / Mourey, L. / Labia, R. / Nicolas-Chanoine, M.H. / Nordmann, P. / Frere, J.M. / Samama, J.P.
#1: Journal: FEMS Microbiol.Lett. / Year: 1996
Title: A Kinetic Study of NMC-A Beta-Lactamase, an Ambler Class A Carbapenemase Also Hydrolyzing Cephamycins
Authors: Mariotte-Boyer, S. / Nicolas-Chanoine, M.H. / Labia, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Analysis of a Carbapenem-Hydrolyzing Class A Beta-Lactamase from Enterobacter Cloacae and of its Lysr-Type Regulatory Protein
Authors: Naas, T. / Nordmann, P.
History
DepositionSep 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE)


Theoretical massNumber of molelcules
Total (without water)29,1381
Polymers29,1381
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.690, 52.900, 67.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE) / CARBAPENEMASE / NMC-A


Mass: 29137.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: NOR-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52663, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 45.6 %
Description: ONE CRYSTAL WAS USED FOR NATIVE LOW RESOLUTION DATA TO 2.9 ANGSTROMS RESOLUTION, AND A SECOND CRYSTAL WAS USED FOR DATA TO 1.64 ANGSTROMS RESOLUTION.
Crystal growpH: 5.25
Details: INITIAL PROTEIN CONCENTRATION WAS 2.0 G/L EQUILIBRATED AGAINST 0.200 M MES PH 5.25, 20% (W/V)PEG 1500, 6% (V/V) N-PROPANOL AT 295K.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 mg/mlprotein1drop
245 mMMES1drop
35 %(w/v)PEG15001drop
4200 mMMES1reservoir
520 %(w/v)PEG15001reservoir
66 %(v/v)n-propyl alcohol1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.64→31 Å / Num. obs: 32762 / % possible obs: 93.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 33.3
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7.1 / Rsym value: 0.192 / % possible all: 68
Reflection
*PLUS
Num. measured all: 111487

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
CCP4model building
X-PLORmodel building
X-PLOR3.1refinement
CCP4data scaling
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: SIRAS
Starting model: NOT APPLICABLE

Resolution: 1.64→31 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT CORRECTION USED WITH A DENSITY OF 0.34 E-/A**3, SOLVENT RADIUS OF 0.25 ANGSTROMS AND B FACTORS OF 50 A**2 RESIDUES 30 AND 63 HAVE ALTERNATE CONFORMATIONS. RESIDUE 140A WAS INSERTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1623 5 %RANDOM
Rwork0.192 ---
obs0.192 32739 93.3 %-
Displacement parametersBiso mean: 13.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 31 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.64→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 0 115 2143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.297
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.126
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: NOT APPLICABLE
LS refinement shellResolution: 1.64→1.71 Å / Total num. of bins used: 8 / % reflection obs: 74.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.126

+
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