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- PDB-4jdn: Secreted Chlamydial Protein PGP3, C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 4jdn
TitleSecreted Chlamydial Protein PGP3, C-terminal Domain
ComponentsVirulence plasmid protein pGP3-D
KeywordsCELL INVASION / virulence factor / secreted protein / chlamydia / inflammatory response / tnf
Function / homologyJelly Rolls - #1340 / Jelly Rolls / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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)48,0295
Polymers47,8973
Non-polymers1312
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-51 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.604, 78.604, 129.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Virulence plasmid protein pGP3-D


Mass: 15965.795 Da / Num. of mol.: 3 / Fragment: C-terminal domain (unp residues 113-264)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D-LC / Gene: pgp3 / Plasmid: pAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7DHH5
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.2 M Na/K phosphate , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 60439 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.115 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4 / Num. unique all: 2999 / Rsym value: 0.436 / % possible all: 98.6

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→37.598 Å / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1910 6.24 %random
Rwork0.1546 ---
obs0.1569 58323 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 2→37.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 7 305 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083271
X-RAY DIFFRACTIONf_angle_d1.1564456
X-RAY DIFFRACTIONf_dihedral_angle_d13.2041177
X-RAY DIFFRACTIONf_chiral_restr0.081545
X-RAY DIFFRACTIONf_plane_restr0.006569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9969-2.02310.23231190.17431861X-RAY DIFFRACTION85
2.0231-2.05090.2251280.17561990X-RAY DIFFRACTION93
2.0509-2.08020.20651430.16562059X-RAY DIFFRACTION94
2.0802-2.11120.18391280.14932015X-RAY DIFFRACTION93
2.1112-2.14420.20151350.15162063X-RAY DIFFRACTION94
2.1442-2.17930.19261350.15642068X-RAY DIFFRACTION94
2.1793-2.21690.2021340.1612035X-RAY DIFFRACTION95
2.2169-2.25720.20741440.16362145X-RAY DIFFRACTION95
2.2572-2.30060.20351410.16382021X-RAY DIFFRACTION94
2.3006-2.34760.20911340.16862066X-RAY DIFFRACTION95
2.3476-2.39860.23081490.16462090X-RAY DIFFRACTION95
2.3986-2.45440.18031430.15762089X-RAY DIFFRACTION96
2.4544-2.51580.20531390.16052105X-RAY DIFFRACTION97
2.5158-2.58380.1931370.1592068X-RAY DIFFRACTION96
2.5838-2.65980.23231380.16572126X-RAY DIFFRACTION97
2.6598-2.74560.21261540.15922166X-RAY DIFFRACTION98
2.7456-2.84370.21420.16112134X-RAY DIFFRACTION98
2.8437-2.95750.2111380.15632147X-RAY DIFFRACTION99
2.9575-3.09210.19981540.15712163X-RAY DIFFRACTION99
3.0921-3.2550.17791450.15172168X-RAY DIFFRACTION99
3.255-3.45880.17021530.14182184X-RAY DIFFRACTION100
3.4588-3.72570.15561460.14462175X-RAY DIFFRACTION100
3.7257-4.10020.20081350.14162177X-RAY DIFFRACTION100
4.1002-4.69250.16251460.12582193X-RAY DIFFRACTION100
4.6925-5.90840.16691440.14622181X-RAY DIFFRACTION100
5.9084-37.60420.17831350.18372195X-RAY DIFFRACTION100

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