[English] 日本語
Yorodumi
- PDB-3rpc: The crystal structure of a possible metal-dependent hydrolase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rpc
TitleThe crystal structure of a possible metal-dependent hydrolase from Veillonella parvula DSM 2008
Componentspossible metal-dependent hydrolase
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyBeta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / metal ion binding / Alpha Beta / Lactamase_B domain-containing protein
Function and homology information
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsTan, K. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible metal-dependent hydrolase from Veillonella parvula DSM 2008
Authors: Tan, K. / Marshall, N. / Clancy, S. / Joachimiak, A.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: possible metal-dependent hydrolase
B: possible metal-dependent hydrolase
C: possible metal-dependent hydrolase
D: possible metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,25212
Polymers118,7294
Non-polymers5238
Water23,4201300
1
A: possible metal-dependent hydrolase
D: possible metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6266
Polymers59,3642
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-165 kcal/mol
Surface area20390 Å2
MethodPISA
2
B: possible metal-dependent hydrolase
C: possible metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6266
Polymers59,3642
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-165 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.859, 97.104, 123.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

-
Components

#1: Protein
possible metal-dependent hydrolase


Mass: 29682.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0210 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D1BQT4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1300 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.49→30 Å / Num. all: 167436 / Num. obs: 167436 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 33.7
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8180 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→30 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 8113 5.03 %random
Rwork0.1579 ---
all0.1591 161443 --
obs0.1591 161443 96.01 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.065 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9415 Å2-0 Å2-0 Å2
2---1.1136 Å20 Å2
3----4.8279 Å2
Refinement stepCycle: LAST / Resolution: 1.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8152 0 8 1300 9460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068429
X-RAY DIFFRACTIONf_angle_d1.03911497
X-RAY DIFFRACTIONf_dihedral_angle_d11.8323107
X-RAY DIFFRACTIONf_chiral_restr0.0691361
X-RAY DIFFRACTIONf_plane_restr0.0041483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4901-1.5070.29562490.27894401X-RAY DIFFRACTION84
1.507-1.52470.28712100.26284610X-RAY DIFFRACTION87
1.5247-1.54330.25012510.23744647X-RAY DIFFRACTION88
1.5433-1.56290.2662280.22814679X-RAY DIFFRACTION89
1.5629-1.58340.262450.22474776X-RAY DIFFRACTION90
1.5834-1.60510.25792790.20484763X-RAY DIFFRACTION91
1.6051-1.62810.23232320.19684916X-RAY DIFFRACTION93
1.6281-1.65240.22582870.19434921X-RAY DIFFRACTION93
1.6524-1.67820.22332640.18884984X-RAY DIFFRACTION95
1.6782-1.70570.24032870.17935047X-RAY DIFFRACTION95
1.7057-1.73510.2192810.16685018X-RAY DIFFRACTION95
1.7351-1.76670.19212330.16925132X-RAY DIFFRACTION96
1.7667-1.80060.19722570.15595096X-RAY DIFFRACTION97
1.8006-1.83740.1942700.15835191X-RAY DIFFRACTION98
1.8374-1.87730.19012880.15435204X-RAY DIFFRACTION98
1.8773-1.9210.19612970.15555200X-RAY DIFFRACTION99
1.921-1.9690.18982980.15185230X-RAY DIFFRACTION99
1.969-2.02230.18652920.15695253X-RAY DIFFRACTION99
2.0223-2.08180.18123140.15435246X-RAY DIFFRACTION99
2.0818-2.1490.17212950.14865278X-RAY DIFFRACTION100
2.149-2.22580.18352840.14995290X-RAY DIFFRACTION100
2.2258-2.31490.17552820.15035343X-RAY DIFFRACTION100
2.3149-2.42020.17062730.14735322X-RAY DIFFRACTION100
2.4202-2.54780.19232660.15585362X-RAY DIFFRACTION100
2.5478-2.70740.19462930.1665361X-RAY DIFFRACTION100
2.7074-2.91640.17922600.16155346X-RAY DIFFRACTION100
2.9164-3.20970.17412740.15755404X-RAY DIFFRACTION100
3.2097-3.67390.14632840.14815394X-RAY DIFFRACTION100
3.6739-4.62750.14952620.12935420X-RAY DIFFRACTION99
4.6275-39.27720.17672780.15925496X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 38.4737 Å / Origin y: -15.3066 Å / Origin z: 0.0965 Å
111213212223313233
T0.0898 Å20.0003 Å20.0039 Å2-0.1312 Å20.0116 Å2--0.1296 Å2
L0.0798 °20.0018 °20.0881 °2-0.2026 °2-0.068 °2--0.4006 °2
S0.0065 Å °-0.0184 Å °-0.0078 Å °-0.0028 Å °0.0213 Å °-0.0047 Å °-0.0418 Å °-0.027 Å °-0.0131 Å °
Refinement TLS groupSelection details: all

+
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