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- PDB-5ue0: 1.90 A resolution structure of CT622 C-terminal domain from Chlam... -

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Basic information

Entry
Database: PDB / ID: 5ue0
Title1.90 A resolution structure of CT622 C-terminal domain from Chlamydia trachomatis
ComponentsCT622 protein
KeywordsPROTEIN BINDING / T3SS effector / helical bundle / prenylation
Function / homologyCHLPN 76kDa-like protein
Function and homology information
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI079083 United States
CitationJournal: Front Cell Infect Microbiol / Year: 2018
Title: The Loss of Expression of a Single Type 3 Effector (CT622) Strongly ReducesChlamydia trachomatisInfectivity and Growth.
Authors: Cosse, M.M. / Barta, M.L. / Fisher, D.J. / Oesterlin, L.K. / Niragire, B. / Perrinet, S. / Millot, G.A. / Hefty, P.S. / Subtil, A.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 25, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CT622 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8482
Polymers31,7521
Non-polymers961
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area12980 Å2
2
A: CT622 protein
hetero molecules

A: CT622 protein
hetero molecules

A: CT622 protein
hetero molecules

A: CT622 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,3938
Polymers127,0094
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6460 Å2
ΔGint-118 kcal/mol
Surface area45860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.812, 121.812, 121.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-701-

SO4

21A-701-

SO4

31A-883-

HOH

41A-895-

HOH

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Components

#1: Protein CT622 protein


Mass: 31752.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria)
Strain: 434/Bu / ATCC VR-902B / Gene: CTL0886 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A0H3MDV9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 7.2), 1.9 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→60.91 Å / Num. obs: 23829 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.6 / CC1/2: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2502: ???)refinement
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.556 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.47
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1135 4.77 %Random selection
Rwork0.2109 ---
obs0.2132 23796 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 5 97 2112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122027
X-RAY DIFFRACTIONf_angle_d1.0652745
X-RAY DIFFRACTIONf_dihedral_angle_d10.8381244
X-RAY DIFFRACTIONf_chiral_restr0.053330
X-RAY DIFFRACTIONf_plane_restr0.008361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.98650.41311400.39282801X-RAY DIFFRACTION100
1.9865-2.09120.3081340.26592821X-RAY DIFFRACTION100
2.0912-2.22220.26931350.23122804X-RAY DIFFRACTION100
2.2222-2.39380.28851590.23462799X-RAY DIFFRACTION100
2.3938-2.63460.26321400.22142822X-RAY DIFFRACTION100
2.6346-3.01560.31151240.22582858X-RAY DIFFRACTION100
3.0156-3.79840.25341400.2092835X-RAY DIFFRACTION100
3.7984-32.56040.21851630.17292921X-RAY DIFFRACTION100
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)
13.99860.9172-1.20064.0658-1.30924.2202-0.35220.3391-0.0164-0.31770.56420.53580.5272-0.4137-0.27290.297-0.0476-0.08310.29140.0630.264551.82438.7918.2129
22.7783-0.1176-1.34724.4506-1.01746.1563-0.50720.55890.2413-0.61270.23991.4578-0.1259-0.6866-0.43440.3397-0.0388-0.21580.49330.09180.641444.210445.983315.3963
33.93051.4816-1.88734.9636-1.61541.9487-0.0329-0.03130.15370.04070.23390.26770.04120.0761-0.21130.17650.0391-0.02520.2553-0.03370.171661.91451.670920.9772
42.7691.02142.15392.30670.93772.85260.0243-0.0431-0.16070.02010.0295-0.39060.0850.0463-0.07710.15870.02570.01230.3067-0.04060.345383.794953.055823.6108
51.44931.43132.73472.6682.25536.3624-0.01380.31980.3236-0.22210.1292-0.53390.02870.13860.1850.2022-0.01640.03470.3836-0.0460.486484.783462.995318.8176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 353 through 404 )
2X-RAY DIFFRACTION2chain 'A' and (resid 405 through 430 )
3X-RAY DIFFRACTION3chain 'A' and (resid 431 through 515 )
4X-RAY DIFFRACTION4chain 'A' and (resid 516 through 613 )
5X-RAY DIFFRACTION5chain 'A' and (resid 614 through 650 )

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