[English] 日本語
Yorodumi
- PDB-2x4a: Crystal structure of the C-terminal domain of InvA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x4a
TitleCrystal structure of the C-terminal domain of InvA
ComponentsINVASION PROTEIN INVA
KeywordsPROTEIN TRANSPORT / TRANSPORT / PATHOGENESIS
Function / homology
Function and homology information


protein secretion / plasma membrane
Similarity search - Function
FHIPEP family, domain 3 / FHIPEP family, domain 2 / FHIPEP family, domain 4 / FHIPEP family, domain 1 / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 ...FHIPEP family, domain 3 / FHIPEP family, domain 2 / FHIPEP family, domain 4 / FHIPEP family, domain 1 / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Ribosomal Protein L9; domain 1 / Helicase, Ruva Protein; domain 3 / Glutaredoxin / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Invasion protein InvA
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWorrall, L.J. / Vuckovic, M. / Strynadka, N.C.J.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal Structure of the C-Terminal Domain of the Salmonella Type III Secretion System Export Apparatus Protein Inva.
Authors: Worrall, L.J. / Vuckovic, M. / Strynadka, N.C.J.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: INVASION PROTEIN INVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5644
Polymers38,1531
Non-polymers4113
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.170, 79.170, 127.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein INVASION PROTEIN INVA


Mass: 38153.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 357-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: LT2 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1I3
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.04 Å3/Da / Density % sol: 59.57 % / Description: NONE
Crystal growpH: 10.5
Details: 0.2 M LISO4, 0.1 M CAPS PH 10.5, 1.2 M NAH2PO4/0.8M K2HPO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 26, 2009 / Details: MIRRORS
RadiationMonochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→68 Å / Num. obs: 15561 / % possible obs: 96.5 % / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4 / % possible all: 76.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X49

2x49


Resolution: 2.54→46.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 19.575 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 779 5 %RANDOM
Rwork0.206 ---
obs0.209 14827 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.37 Å20 Å2
2--0.73 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.54→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 24 78 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222712
X-RAY DIFFRACTIONr_bond_other_d0.0010.021871
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9843665
X-RAY DIFFRACTIONr_angle_other_deg0.99434556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0523.643129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36215509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7661525
X-RAY DIFFRACTIONr_chiral_restr0.0970.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.51637
X-RAY DIFFRACTIONr_mcbond_other0.1651.5664
X-RAY DIFFRACTIONr_mcangle_it1.45822655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.37131075
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7354.51009
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 58 -
Rwork0.301 960 -
obs--90.89 %
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)
15.94061.61951.59611.55491.01280.91420.10810.4450.382-0.1428-0.0926-0.2573-0.20930.049-0.01550.14960.02030.00650.14890.09820.169350.295-13.489-2.564
22.8618-2.32970.93163.3935-1.41.6414-0.0436-0.02360.03340.1313-0.0051-0.0818-0.06140.0960.04860.10080.00340.01240.14110.00530.085455.24-19.6918.808
35.71090.49953.3562.4107-0.11014.0496-0.10650.16110.2954-0.17690.0090.394-0.1886-0.37880.09750.1233-0.0185-0.00660.1533-0.01080.129223.104-15.5145.63
43.15720.57181.63473.6710.04474.9355-0.0744-0.08870.0692-0.2599-0.03420.4035-0.1511-0.38150.10850.1584-0.0067-0.01270.13310.04820.132234.911-21.86225.884
55.6283-0.3489-0.24732.9993-1.51234.90390.03230.0929-0.24180.0347-0.0773-0.10880.21550.1210.0450.1234-0.00030.0170.09690.00320.028339.516-24.39621.57
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 393
2X-RAY DIFFRACTION2A394 - 496
3X-RAY DIFFRACTION3A497 - 571
4X-RAY DIFFRACTION4A572 - 631
5X-RAY DIFFRACTION5A632 - 685

+
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