[English] 日本語
Yorodumi
- PDB-4jdo: Secreted chlamydial protein pgp3, coiled-coil deletion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jdo
TitleSecreted chlamydial protein pgp3, coiled-coil deletion
ComponentsVirulence plasmid protein pGP3-D
KeywordsCELL INVASION / virulence factor / secreted protein / chlamydia / inflammatory response / tnf
Function / homology
Function and homology information


: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #20 / Chlamydia virulence plasmid protein pGP3 / pGP3 C-terminal domain / Pgp3 C-terminal domain / Jelly Rolls - #1340 / Other non-globular / Special / Jelly Rolls ...: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #20 / Chlamydia virulence plasmid protein pGP3 / pGP3 C-terminal domain / Pgp3 C-terminal domain / Jelly Rolls - #1340 / Other non-globular / Special / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Virulence plasmid protein pGP3-D
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGalaleldeen, A. / Taylor, A.B. / Chen, D. / Holloway, S.P. / Zhong, G. / Hart, P.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Chlamydia trachomatis immunodominant antigen Pgp3.
Authors: Galaleldeen, A. / Taylor, A.B. / Chen, D. / Schuermann, J.P. / Holloway, S.P. / Hou, S. / Gong, S. / Zhong, G. / Hart, P.J.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Virulence plasmid protein pGP3-D
B: Virulence plasmid protein pGP3-D
C: Virulence plasmid protein pGP3-D
D: Virulence plasmid protein pGP3-D
E: Virulence plasmid protein pGP3-D
F: Virulence plasmid protein pGP3-D
G: Virulence plasmid protein pGP3-D
H: Virulence plasmid protein pGP3-D
I: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,82812
Polymers208,7599
Non-polymers693
Water12,863714
1
A: Virulence plasmid protein pGP3-D
B: Virulence plasmid protein pGP3-D
C: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6094
Polymers69,5863
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15080 Å2
ΔGint-111 kcal/mol
Surface area23860 Å2
MethodPISA
2
D: Virulence plasmid protein pGP3-D
E: Virulence plasmid protein pGP3-D
F: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6094
Polymers69,5863
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-110 kcal/mol
Surface area23950 Å2
MethodPISA
3
G: Virulence plasmid protein pGP3-D
H: Virulence plasmid protein pGP3-D
I: Virulence plasmid protein pGP3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6094
Polymers69,5863
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-113 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.240, 146.240, 160.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
Virulence plasmid protein pGP3-D


Mass: 23195.436 Da / Num. of mol.: 9 / Fragment: N-terminal and C-terminal domain fusion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: ERS082928_02094 / Plasmid: pAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E9CJA7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / pH: 7
Details: 20% PEG 6000, 0.1 M tri-sodium citrate , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97928
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 86176 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.132 / Net I/σ(I): 14.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.573 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JDN

4jdn


Resolution: 2.3→29.46 Å / SU ML: 0.3 / Isotropic thermal model: isotropic / σ(F): 1.92 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 4312 5.01 %
Rwork0.184 --
obs0.187 81677 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14307 0 3 714 15024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914525
X-RAY DIFFRACTIONf_angle_d1.26819757
X-RAY DIFFRACTIONf_dihedral_angle_d14.5185199
X-RAY DIFFRACTIONf_chiral_restr0.0822434
X-RAY DIFFRACTIONf_plane_restr0.0052527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3021-2.32820.35012860.25675247X-RAY DIFFRACTION98
2.3282-2.35560.31872900.24385425X-RAY DIFFRACTION100
2.3556-2.38430.31273250.24495361X-RAY DIFFRACTION100
2.3843-2.41450.31372710.2425395X-RAY DIFFRACTION100
2.4145-2.44630.32742860.23865441X-RAY DIFFRACTION100
2.4463-2.47970.27123020.2265432X-RAY DIFFRACTION100
2.4797-2.51520.26982450.21445345X-RAY DIFFRACTION100
2.5152-2.55270.31092840.21335408X-RAY DIFFRACTION100
2.5527-2.59250.31082260.21685446X-RAY DIFFRACTION100
2.5925-2.6350.25262760.21475438X-RAY DIFFRACTION100
2.635-2.68040.30762740.21595388X-RAY DIFFRACTION100
2.6804-2.72910.27172860.20775383X-RAY DIFFRACTION100
2.7291-2.78160.27713180.19425427X-RAY DIFFRACTION100
2.7816-2.83830.26852820.20865310X-RAY DIFFRACTION100
2.8383-2.90.3162660.22185464X-RAY DIFFRACTION100
2.9-2.96740.26463230.19935340X-RAY DIFFRACTION100
2.9674-3.04150.26073010.18755399X-RAY DIFFRACTION100
3.0415-3.12370.2473080.18495390X-RAY DIFFRACTION100
3.1237-3.21550.26292760.18885350X-RAY DIFFRACTION100
3.2155-3.31910.23472930.18625442X-RAY DIFFRACTION100
3.3191-3.43760.25252560.18735396X-RAY DIFFRACTION100
3.4376-3.5750.22092830.18015466X-RAY DIFFRACTION100
3.575-3.73740.21213000.16235359X-RAY DIFFRACTION100
3.7374-3.9340.19823060.16585398X-RAY DIFFRACTION100
3.934-4.17980.20232570.1575434X-RAY DIFFRACTION100
4.1798-4.50150.16052380.13185389X-RAY DIFFRACTION100
4.5015-4.95260.18442920.13755386X-RAY DIFFRACTION100
4.9526-5.66480.21272920.15725424X-RAY DIFFRACTION100
5.6648-7.12040.24282990.17525372X-RAY DIFFRACTION100
7.1204-29.46710.20372860.16755161X-RAY DIFFRACTION96

+
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