[English] 日本語
Yorodumi
- PDB-3nkz: The crystal structure of a flagella protein from Yersinia enteroc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nkz
TitleThe crystal structure of a flagella protein from Yersinia enterocolitica subsp. enterocolitica 8081
ComponentsFlagellar protein fliT
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / protein folding / cytosol
Similarity search - Function
Flagellar protein flit. / Flagellar protein FliT / Flagellar protein FliT / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar protein FliT
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.112 Å
AuthorsTan, K. / Li, H. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a flagella protein from Yersinia enterocolitica subsp. enterocolitica 8081
Authors: Tan, K. / Li, H. / Feldmann, B. / Joachimiak, A.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar protein fliT
B: Flagellar protein fliT
C: Flagellar protein fliT
D: Flagellar protein fliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,51510
Polymers56,7424
Non-polymers7736
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-150 kcal/mol
Surface area19080 Å2
MethodPISA
2
A: Flagellar protein fliT
B: Flagellar protein fliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7575
Polymers28,3712
Non-polymers3863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-68 kcal/mol
Surface area10350 Å2
MethodPISA
3
C: Flagellar protein fliT
D: Flagellar protein fliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7575
Polymers28,3712
Non-polymers3863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-64 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.798, 66.758, 137.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. The chains A and B, C and D likely form dimers, respectively.

-
Components

#1: Protein
Flagellar protein fliT


Mass: 14185.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria)
Strain: 8081 / Gene: fliT, YE2526 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: A1JSR8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.0M Ammonium sulfate, 0.1M Bis-Tris, 1% w/v PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.112→39 Å / Num. all: 34714 / Num. obs: 34714 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 31.9
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.44 / Num. unique all: 1740 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.112→38.936 Å / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1747 5.23 %random
Rwork0.1588 ---
all0.1582 33376 --
obs0.1582 33376 92.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.954 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.3713 Å20 Å20 Å2
2--1.402 Å2-0 Å2
3---5.9693 Å2
Refinement stepCycle: LAST / Resolution: 2.112→38.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 46 87 3218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083172
X-RAY DIFFRACTIONf_angle_d1.0514275
X-RAY DIFFRACTIONf_dihedral_angle_d19.2811229
X-RAY DIFFRACTIONf_chiral_restr0.059526
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1132-2.18140.31151280.25082565X-RAY DIFFRACTION80
2.1814-2.25930.28521290.22672639X-RAY DIFFRACTION82
2.2593-2.34980.2461430.21242737X-RAY DIFFRACTION84
2.3498-2.45670.22351460.21262765X-RAY DIFFRACTION86
2.4567-2.58610.23321530.19932797X-RAY DIFFRACTION87
2.5861-2.7480.21421500.18872869X-RAY DIFFRACTION88
2.748-2.96010.22251630.18982883X-RAY DIFFRACTION88
2.9601-3.25760.22171600.16582980X-RAY DIFFRACTION91
3.2576-3.72820.17141540.13513090X-RAY DIFFRACTION94
3.7282-4.69430.13211510.10973168X-RAY DIFFRACTION95
4.6943-30.05080.16851750.13823212X-RAY DIFFRACTION92
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)
10.3890.1142-0.12780.10070.09060.3368-0.1272-0.02510.0068-0.0630.16490.2819-0.06240.0021-0.04210.29490.03980.05760.03370.02160.3001-6.7335-9.136734.1973
20.37790.0325-0.20431.1992-0.05210.5077-0.1677-0.1481-0.07080.29980.2018-0.33830.10950.0671-0.00890.3710.061-0.00610.05470.02580.23451.5042-13.125140.5672
30.31320.17190.00940.2792-0.09710.17740.13490.0409-0.17370.0692-0.06830.03050.06120.0043-0.04990.27450.0164-0.00370.1906-0.05650.3289.0917-23.0372-0.0456
41.57530.1520.09120.5255-0.2090.13810.1390.31570.1507-0.0105-0.05620.03060.07160.0199-0.05930.25090.0356-0.01890.2226-0.02370.22555.3466-14.6539-6.1096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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