[English] 日本語
Yorodumi
- PDB-3u07: Crystal Structure of the VPA0106 protein from Vibrio parahaemolyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u07
TitleCrystal Structure of the VPA0106 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR106.
Componentsuncharacterized protein VPA0106
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / NESG / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Jelly Rolls - #1600 / Domain of unknown function DUF1254 / Domain of unknown function DUF1254 superfamily / Protein of unknown function (DUF1254) / Domain of unknown function DUF1214 / Protein of unknown function (DUF1214) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF1254 domain-containing protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.083 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the VPA0106 protein from Vibrio parahaemolyticus.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein VPA0106
B: uncharacterized protein VPA0106
C: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)153,4523
Polymers153,4523
Non-polymers00
Water14,052780
1
A: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)51,1511
Polymers51,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)51,1511
Polymers51,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)51,1511
Polymers51,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.445, 96.320, 100.540
Angle α, β, γ (deg.)60.610, 80.870, 86.550
Int Tables number1
Space group name H-MP1
Detailsmonomer,55.15 kD,94.5%

-
Components

#1: Protein uncharacterized protein VPA0106


Mass: 51150.629 Da / Num. of mol.: 3 / Mutation: R60E, I64R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA0106 / Plasmid: pET21_NESG, VpR106-RM.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q87JZ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 6
Details: 20% PEG 4000, 0.1M sodium nitrate, 0.1M MES, pH 6.0, Microbatch crystallization under oil, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.083→50 Å / Num. all: 198295 / Num. obs: 188380 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 25.05 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 2.8 / Num. unique all: 19654 / % possible all: 79.8

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.083→46.958 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.6 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 9413 5 %
Rwork0.194 --
obs0.195 188331 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.226 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 124.28 Å2 / Biso mean: 32.622 Å2 / Biso min: 1.71 Å2
Baniso -1Baniso -2Baniso -3
1--5.148 Å20.733 Å20.897 Å2
2--0.266 Å22.341 Å2
3---4.881 Å2
Refinement stepCycle: LAST / Resolution: 2.083→46.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9549 0 0 780 10329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069789
X-RAY DIFFRACTIONf_angle_d1.40313255
X-RAY DIFFRACTIONf_chiral_restr0.1041377
X-RAY DIFFRACTIONf_plane_restr0.0061741
X-RAY DIFFRACTIONf_dihedral_angle_d14.8513633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.083-2.1070.3071620.263356351853
2.107-2.1310.2962490.2554896514577
2.131-2.1570.3062880.2475558584688
2.157-2.1850.2893040.2345997630196
2.185-2.2140.263110.2416034634597
2.214-2.2440.2433000.2226198649897
2.244-2.2760.2243160.2245983629997
2.276-2.310.2423320.2266083641597
2.31-2.3460.2943300.2226152648297
2.346-2.3840.2683490.2145947629697
2.384-2.4250.2443010.2116241654297
2.425-2.470.2593230.2166016633997
2.47-2.5170.2482690.2136079634897
2.517-2.5680.2313690.2216209657897
2.568-2.6240.2553160.2236022633897
2.624-2.6850.2643080.2136179648797
2.685-2.7530.2493070.2146097640497
2.753-2.8270.243440.2096144648898
2.827-2.910.2563040.2116152645697
2.91-3.0040.2563080.2156191649998
3.004-3.1110.2173640.216080644498
3.111-3.2360.2143120.1976190650298
3.236-3.3830.2153320.1936092642498
3.383-3.5610.193060.1856164647098
3.561-3.7840.1953380.1816142648098
3.784-4.0760.1933480.1636167651598
4.076-4.4860.1583360.146163649998
4.486-5.1350.1433500.146170652098
5.135-6.4670.1763110.186165647698
6.467-46.970.2043260.1926051637796
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00210.00010.0030.0016-0.00480.00560.01480.0001-0.019-0.00980.0216-0.00580.01660.011300.06570.0196-0.00190.10620.0815-0.0003-0.2691-0.268-0.2038
20.0018-0.00030.00040.00390.0050.002-0.00270.01830.0074-0.0071-0.0146-0.0169-0.0125-0.0085-00.06610.0046-0.00010.0347-0.10220.07930.058940.612126.7507
30.00120.00410.00080.00550.0012-0.001-0.0039-0.00670.01860.0089-0.01070.00650.00140.00980-0.0018-0.04590.0079-0.04180.02350.0454-0.0887-3.003648.7101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA25 - 435
2X-RAY DIFFRACTION2chain BB25 - 435
3X-RAY DIFFRACTION3chain CC25 - 435

+
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