[English] 日本語
Yorodumi
- PDB-1m6k: Structure of the OXA-1 class D beta-lactamase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m6k
TitleStructure of the OXA-1 class D beta-lactamase
Componentsbeta-lactamase OXA-1
KeywordsHYDROLASE / side chain modification / lysine carbamylation / hydrolysis
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase OXA-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSun, T. / Nukaga, M. / Mayama, K. / Braswell, E.H. / Knox, J.R.
Citation
Journal: PROTEIN SCI. / Year: 2003
Title: Comparison of beta-lactamases of classes A and D: 1.5A crystallographic structure of the class D OXA-1 oxacillinase
Authors: Sun, T. / Nukaga, M. / Mayama, K. / Braswell, E.H. / Knox, J.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray study of OXA-1, a class D beta-lactamase
Authors: Sun, T. / Nukaga, M. / Mayama, K. / Crichlow, G.V. / Kuzin, A.P. / Knox, J.R.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE AUTHORS STATE THAT THE MATURE, CRYSTALLIZED PROTEIN STARTS AT RESIDUE 18 AS CONFIRMED BY ...SEQUENCE AUTHORS STATE THAT THE MATURE, CRYSTALLIZED PROTEIN STARTS AT RESIDUE 18 AS CONFIRMED BY SEQUENCING. RESIDUES 16 AND 17 ARE IN THE SIGNAL SEQUENCE. AUTHORS ALSO STATE THAT ARG 128 IS AN ERROR IN THE SWISSPROT SEQUENCE AND THAT GLY 128 IS THE CORRECT RESIDUE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-lactamase OXA-1
B: beta-lactamase OXA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,58912
Polymers56,4082
Non-polymers1,18210
Water10,070559
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.02, 51.62, 72.89
Angle α, β, γ (deg.)70.19, 84.11, 81.51
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein beta-lactamase OXA-1 / Penicillinase / oxacillinase


Mass: 28203.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OXA1 / Plasmid: pET12a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P13661, beta-lactamase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000 (10/20%), 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.5-3 mg/mlprotein1drop
210 %PEG80001drop
30.05 MHEPES1droppH7.5
420 %PEG80001reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.935
SYNCHROTRONCHESS A120.929
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 13, 1999
ADSC QUANTUM 42CCDJun 8, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1crystalSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9351
20.9291
ReflectionResolution: 1.49→50 Å / Num. all: 69837 / Num. obs: 69837 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 23.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2979 / Rsym value: 0.123 / % possible all: 36.9
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. obs: 69838 / Redundancy: 2.62 % / Num. measured all: 183270
Reflection shell
*PLUS
% possible obs: 36.9 % / Redundancy: 1.53 % / Num. unique obs: 2979 / Num. measured obs: 4561 / Mean I/σ(I) obs: 5.3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1FOF and 1E4D

1fof

1e4d


Resolution: 1.5→48.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 500 / Data cutoff high rms absF: 500 / Isotropic thermal model: isotropic B-factors / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1396 1.8 %RANDOM
Rwork0.182 ---
all0.182 68784 --
obs0.182 68784 88.1 %-
Displacement parametersBiso mean: 16.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.184 Å0.161 Å
Luzzati d res low-5 Å
Luzzati sigma a0.081 Å0.089 Å
Refinement stepCycle: LAST / Resolution: 1.5→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3931 0 0 639 4570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.0391.5
X-RAY DIFFRACTIONc_mcangle_it1.5742
X-RAY DIFFRACTIONc_scbond_it1.8082
X-RAY DIFFRACTIONc_scangle_it2.6442.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.225 91 3 %
Rwork0.212 2979 -
obs-3795 48.7 %
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 75 Å / Num. reflection obs: 67388 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.222 / Rfactor Rwork: 0.215

+
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://pdbjlvh1.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