[English] 日本語
Yorodumi
- PDB-4gqz: Crystal Structure of S.CueP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gqz
TitleCrystal Structure of S.CueP
ComponentsPutative periplasmic or exported protein
KeywordsMETAL BINDING PROTEIN / CueP / V-shape dimer / Copper_resistance
Function / homologyImmunoglobulin-like - #3700 / Immunoglobulin-like / Sandwich / Mainly Beta / Putative periplasmic or exported protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.799 Å
AuthorsHa, N.C. / Yoon, B.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium
Authors: Yoon, B.-Y. / Kim, Y.-H. / Kim, N. / Yun, B.-Y. / Kim, J.-S. / Lee, J.-H. / Cho, H.-S. / Lee, K. / Ha, N.-C.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative periplasmic or exported protein
B: Putative periplasmic or exported protein
C: Putative periplasmic or exported protein
D: Putative periplasmic or exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7856
Polymers71,7144
Non-polymers712
Water8,719484
1
A: Putative periplasmic or exported protein
B: Putative periplasmic or exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8923
Polymers35,8572
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-17 kcal/mol
Surface area14610 Å2
MethodPISA
2
C: Putative periplasmic or exported protein
D: Putative periplasmic or exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8923
Polymers35,8572
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-17 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.456, 102.160, 114.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Putative periplasmic or exported protein / CueP


Mass: 17928.455 Da / Num. of mol.: 4 / Fragment: UNP residues 21-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM3650 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZL99
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2.0M sodium chloride , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9790, 0.9792, 0.9900
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: double mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.991
ReflectionResolution: 1.799→50 Å / Num. obs: 118693 / % possible obs: 19.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.89 Å2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 81.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.799→40.854 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.746 / SU ML: 0.23 / σ(F): 1.45 / Phase error: 31.71 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 3679 3.1 %random
Rwork0.2279 ---
obs0.2294 118692 96.75 %-
all-122680 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 25.8548 Å2 / Biso min: 12.86 Å2
Refinement stepCycle: LAST / Resolution: 1.799→40.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4915 0 2 484 5401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085046
X-RAY DIFFRACTIONf_angle_d1.126852
X-RAY DIFFRACTIONf_chiral_restr0.081766
X-RAY DIFFRACTIONf_plane_restr0.005888
X-RAY DIFFRACTIONf_dihedral_angle_d16.2821848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7993-1.8230.34191000.33863257335771
1.823-1.84790.31241230.33713803392684
1.8479-1.87430.35421310.32274041417288
1.8743-1.90230.36921380.31384251438993
1.9023-1.9320.38011400.28964382452296
1.932-1.96370.29731490.28094488463798
1.9637-1.99760.30671420.27164476461898
1.9976-2.03390.32491360.25594507464399
2.0339-2.0730.31531480.24624561470999
2.073-2.11530.27511460.23014468461499
2.1153-2.16130.25311440.23214572471699
2.1613-2.21160.29971470.22524540468799
2.2116-2.26690.2781490.21694527467699
2.2669-2.32820.28671440.22314536468099
2.3282-2.39670.29551460.228145184664100
2.3967-2.4740.34631440.233945764720100
2.474-2.56240.25361480.222545784726100
2.5624-2.6650.2981430.222145424685100
2.665-2.78630.25161480.226545724720100
2.7863-2.93310.30431450.229745274672100
2.9331-3.11680.27771420.224745674709100
3.1168-3.35740.31991480.212545504698100
3.3574-3.69510.27851410.201245664707100
3.6951-4.22930.23471520.191245774729100
4.2293-5.32660.20371470.189245594706100
5.3266-40.86420.23781380.25054472461098

+
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