[English] 日本語
Yorodumi
- PDB-1zvp: Crystal Structure of a Protein of Unknown Function VC0802 from Vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zvp
TitleCrystal Structure of a Protein of Unknown Function VC0802 from Vibrio cholerae, Possible Transport Protein
Componentshypothetical protein VC0802
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio cholerae / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity
Similarity search - Function
Domain of unknown function DUF2241 / ACT domain / VC0802-like / CASTOR, ACT domain / ACT domain / VC0802-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, R. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a hypothetical protein VC0802 from Vibrio cholerae
Authors: Zhang, R. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein VC0802
B: hypothetical protein VC0802
C: hypothetical protein VC0802
D: hypothetical protein VC0802


Theoretical massNumber of molelcules
Total (without water)56,6204
Polymers56,6204
Non-polymers00
Water5,801322
1
A: hypothetical protein VC0802
D: hypothetical protein VC0802


Theoretical massNumber of molelcules
Total (without water)28,3102
Polymers28,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-29 kcal/mol
Surface area11960 Å2
MethodPISA
2
B: hypothetical protein VC0802
C: hypothetical protein VC0802


Theoretical massNumber of molelcules
Total (without water)28,3102
Polymers28,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-27 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.224, 99.561, 163.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThis protein existed as dimer. MolA+MolD, MolB+MolC are two dimers in asymmetric unit.

-
Components

#1: Protein
hypothetical protein VC0802


Mass: 14155.044 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: GI:9655251 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 9655251, UniProt: Q9KTT6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.257 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 45% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 21, 2004 / Details: mirriors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40583 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 21.11 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.44
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.28 / Num. unique all: 7744 / % possible all: 72.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→81.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 21.114 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.188
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24643 1953 5 %RANDOM
Rwork0.21404 ---
obs0.21573 37076 96.27 %-
all-38512 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.146 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 0 322 4190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223931
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9785324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28725.987157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76715663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.433154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022890
X-RAY DIFFRACTIONr_nbd_refined0.2030.21645
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.212
X-RAY DIFFRACTIONr_mcbond_it0.6561.52595
X-RAY DIFFRACTIONr_mcangle_it1.21524038
X-RAY DIFFRACTIONr_scbond_it1.28831462
X-RAY DIFFRACTIONr_scangle_it2.34.51286
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 115 -
Rwork0.384 2062 -
obs--73.37 %
Refinement TLS params.Method: refined / Origin x: 32.521 Å / Origin y: 30.415 Å / Origin z: 61.612 Å
111213212223313233
T0.0983 Å20.125 Å2-0.0192 Å2--0.0184 Å20.0262 Å2---0.1388 Å2
L1.9116 °2-1.6512 °2-0.6938 °2-2.3107 °20.7953 °2--0.2952 °2
S0.0307 Å °0.0109 Å °0.0106 Å °-0.0318 Å °-0.0096 Å °-0.0224 Å °-0.0214 Å °-0.0005 Å °-0.021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 683 - 69
2X-RAY DIFFRACTION1AA69 - 13170 - 132
3X-RAY DIFFRACTION1BB2 - 683 - 69
4X-RAY DIFFRACTION1BB69 - 13170 - 132
5X-RAY DIFFRACTION1CC0 - 681 - 69
6X-RAY DIFFRACTION1CC69 - 12970 - 130
7X-RAY DIFFRACTION1DD1 - 682 - 69
8X-RAY DIFFRACTION1DD69 - 13170 - 132

+
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