[English] 日本語
Yorodumi
- PDB-6nj1: Crystal structure of class A beta-lactamase from Clostridium kluy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nj1
TitleCrystal structure of class A beta-lactamase from Clostridium kluyveri DSM 555
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 active site / Beta-lactamase class-A active site. / 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
Biological speciesClostridium kluyveri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.399 Å
AuthorsMichalska, K. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of class A beta-lactamase from Clostridium kluyveri DSM 555
Authors: Michalska, K. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1416
Polymers30,9631
Non-polymers1775
Water3,873215
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,28112
Polymers61,9272
Non-polymers35510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+5/31
Buried area1970 Å2
ΔGint-101 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.878, 66.878, 119.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-402-

CL

21A-534-

HOH

-
Components

#1: Protein Beta-lactamase


Mass: 30963.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NCIMB 10680) (bacteria)
Strain: ATCC 8527 / DSM 555 / NCIMB 10680 / Gene: bla, CKL_2902 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5N1B8, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1 M LiCl, 0.1 M sodium citrate pH 4.0, 20% PEG6000, cryo 15% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 9, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 118279 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 24.627
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.676 / Mean I/σ(I) obs: 1.332 / Num. unique obs: 3040 / CC1/2: 0.709 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(dev_2947: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.399→29.197 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 14.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1512 5758 4.87 %
Rwork0.1235 --
obs0.1249 118223 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→29.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 5 215 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122085
X-RAY DIFFRACTIONf_angle_d1.222832
X-RAY DIFFRACTIONf_dihedral_angle_d16.091776
X-RAY DIFFRACTIONf_chiral_restr0.092324
X-RAY DIFFRACTIONf_plane_restr0.008369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.41490.26221860.23333722X-RAY DIFFRACTION98
1.4149-1.43150.25051970.21033700X-RAY DIFFRACTION100
1.4315-1.4490.22791770.213780X-RAY DIFFRACTION100
1.449-1.46730.25461710.19163719X-RAY DIFFRACTION100
1.4673-1.48660.22271750.18853868X-RAY DIFFRACTION100
1.4866-1.5070.21671750.1733707X-RAY DIFFRACTION100
1.507-1.52850.19312150.15733760X-RAY DIFFRACTION100
1.5285-1.55130.19641700.14653753X-RAY DIFFRACTION100
1.5513-1.57560.19932090.14823734X-RAY DIFFRACTION100
1.5756-1.60140.17142080.13243751X-RAY DIFFRACTION100
1.6014-1.6290.17561850.12443766X-RAY DIFFRACTION100
1.629-1.65860.1581800.11673709X-RAY DIFFRACTION100
1.6586-1.69050.15751980.113766X-RAY DIFFRACTION100
1.6905-1.7250.13481740.10493801X-RAY DIFFRACTION100
1.725-1.76250.15372180.10813736X-RAY DIFFRACTION100
1.7625-1.80350.15671740.10323746X-RAY DIFFRACTION100
1.8035-1.84860.13841900.1053746X-RAY DIFFRACTION100
1.8486-1.89860.15061580.09763809X-RAY DIFFRACTION100
1.8986-1.95450.12692230.09693689X-RAY DIFFRACTION100
1.9545-2.01750.1181840.0993790X-RAY DIFFRACTION100
2.0175-2.08960.13152060.09983731X-RAY DIFFRACTION100
2.0896-2.17330.13271890.10593753X-RAY DIFFRACTION100
2.1733-2.27210.14051980.10763739X-RAY DIFFRACTION100
2.2721-2.39190.14932420.11123712X-RAY DIFFRACTION100
2.3919-2.54170.13792380.11123710X-RAY DIFFRACTION100
2.5417-2.73780.13731560.12083772X-RAY DIFFRACTION100
2.7378-3.0130.15671660.12983763X-RAY DIFFRACTION100
3.013-3.44840.15522100.13453754X-RAY DIFFRACTION100
3.4484-4.34240.13741880.1133720X-RAY DIFFRACTION100
4.3424-29.20360.16231980.14583759X-RAY DIFFRACTION100

+
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://pdbjlc1.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