[English] 日本語
Yorodumi
- PDB-1a7t: METALLO-BETA-LACTAMASE WITH MES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7t
TitleMETALLO-BETA-LACTAMASE WITH MES
ComponentsMETALLO-BETA-LACTAMASE
KeywordsHYDROLASE / HYDROLASE (BETA-LACTAMASE) / METALLO BETA-LACTAMASE / ZINC
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 4-Layer Sandwich / Alpha Beta
Metallo-beta-lactamase type 2
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsFitzgerald, P.M.D. / Wu, J.K. / Toney, J.H.
Citation
Journal: Biochemistry / Year: 1998
Title: Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
Authors: Fitzgerald, P.M. / Wu, J.K. / Toney, J.H.
#1: Journal: Protein Expr.Purif. / Year: 1997
Title: High-Yield Expression, Purification, and Characterization of Active, Soluble Bacteroides Fragilis Metallo-Beta-Lactamase, Ccra
Authors: Toney, J.H. / Wu, J.K. / Overbye, K.M. / Thompson, C.M. / Pompliano, D.L.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 17, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METALLO-BETA-LACTAMASE
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,47310
Polymers50,7752
Non-polymers6988
Water6,071337
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)42.270, 66.960, 69.480
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide METALLO-BETA-LACTAMASE / CLASS B BETA-LACTAMASE


Mass: 25387.666 Da / Num. of mol.: 2 / Mutation: A171T, D208N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: TAL3636 / Gene: CCRA / Variant: CLINICAL ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P25910, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growpH: 6.1
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 100 MM POTASSIUM ACETATE, 100 MM MES, PH 6.1
Crystal grow
*PLUS
pH: 6.3 / Method: unknown
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
110 mg/mlenzyme1
210 mMsodium cacodylate1
32 mMdithiothreitol1
43 mMsodium azide1
5100 mMMES2
6100 mMpotassium acetate2
718-21 %PEG40002

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 5, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 29508 / % possible obs: 91.3 % / Observed criterion σ(I): 1 / Redundancy: 2.06 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 42.8
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 1.47 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.074 / % possible all: 73.9
Reflection shell
*PLUS
% possible obs: 73.9 % / Num. unique obs: 3950

-
Processing

Software
NameClassification
PHASESphasing
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.85→10 Å / σ(F): 1
Details: INITIAL CYCLES OF REFINEMENT WERE PERFORMED USING PROGRAM X-PLOR. 10% OF THE DATA (RANDOMLY SELECTED) WERE SET ASIDE FOR CALCULATION OF A FREE R-FACTOR. AT THE END OF THE X-PLOR PHASE OF THE REFINEMENT, THE WORKING R WAS 0.173 AND R-FREE WAS 0.242.
RfactorNum. reflection% reflection
Rwork0.151 --
Obs-29267 91.3 %
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 30 337 4222
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0180.02
p_angle_d0.0350.03
p_angle_deg
p_planar_d0.0370.04
p_hb_or_metal_coord
p_mcbond_it0.961
p_mcangle_it1.5341.5
p_scbond_it1.4541
p_scangle_it2.3991.5
p_plane_restr0.0170.02
p_chiral_restr0.1660.15
p_singtor_nbd0.2030.5
p_multtor_nbd0.2010.5
p_xhyhbond_nbd
p_xyhbond_nbd0.1990.5
p_planar_tor2.93
p_staggered_tor15.520
p_orthonormal_tor
p_transverse_tor2220
p_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.93 Å / Total num. of bins used: 12 / Num. reflection obs: 2722 / Rfactor obs: 0.188

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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