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- PDB-3qh6: 1.8A resolution structure of CT296 from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 3qh6
Title1.8A resolution structure of CT296 from Chlamydia trachomatis
ComponentsCT296
KeywordsUNKNOWN FUNCTION / CT296 / Iron / modeling / Chlamydia
Function / homologyDomain of unknown function (DUF5070) / Protein of unknown function DUF5070 / Domain of unknown function (DUF5070) / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKemege, K. / Hickey, J. / Lovell, S. / Battaile, K.P. / Zhang, Y. / Hefty, P.S.
CitationJournal: J.Bacteriol. / Year: 2011
Title: Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes.
Authors: Kemege, K.E. / Hickey, J.M. / Lovell, S. / Battaile, K.P. / Zhang, Y. / Hefty, P.S.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CT296
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3462
Polymers18,1521
Non-polymers1941
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CT296
hetero molecules

A: CT296
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6924
Polymers36,3042
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.160, 64.045, 46.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CT296


Mass: 18151.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: L2/434/Bu / Gene: CTL0548 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0B7L2, UniProt: A0A0H3MBY2*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.1 M HEPES, 15 % PEG 20000, pH 7.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.102
ReflectionResolution: 1.8→30 Å / Num. all: 14764 / Num. obs: 14764 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 25.381
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.298 / Rsym value: 0.594 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å23.13 Å
Translation2.5 Å23.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIX1.7_648refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.129 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 0 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 734 5.03 %RANDOM
Rwork0.1975 ---
obs0.1991 14583 99.6 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.535 Å2 / ksol: 0.426 e/Å3
Displacement parametersBiso max: 91.49 Å2 / Biso mean: 30.0284 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--10.3047 Å2-0 Å20 Å2
2---4.723 Å2-0 Å2
3---15.0277 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 13 70 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121154
X-RAY DIFFRACTIONf_angle_d1.2341554
X-RAY DIFFRACTIONf_chiral_restr0.085172
X-RAY DIFFRACTIONf_plane_restr0.006196
X-RAY DIFFRACTIONf_dihedral_angle_d13.771421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.9390.33461530.270627252878100
1.939-2.1340.25171410.227322873100
2.134-2.44250.25461590.19427282887100
2.4425-3.07610.23961200.20072785290599
3.0761-23.13090.19171610.1852879304099
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)
10.3264-0.08110.09530.6191-0.08990.55450.09760.20130.0710.0932-0.0718-0.1076-0.0426-0.0632-0.02410.19840.00380.00860.21220.03180.206-0.300630.9265-2.6917
20.3144-0.0837-0.13630.06560.04460.5149-0.0780.00770.11410.1170.0579-0.0725-0.1984-0.1666-0.09950.12430.03630.03080.1505-0.01030.15916.115823.75565.8446
30.4218-0.1181-0.1420.1276-0.06780.1677-0.03540.0657-0.28370.0153-0.01870.09440.0091-0.01810.03280.16060.00960.01170.1760.02720.26580.029514.29784.3315
40.3693-0.07990.14060.17670.02670.78720.06920.1423-0.101-0.08010.0537-0.01590.28790.0152-0.04250.17950.0047-0.0040.1696-0.0090.16167.073312.37031.2971
50.05610.21280.11860.84210.49480.6103-0.0137-0.08460.07280.08750.0423-0.2779-0.21260.0515-0.01430.17960.02-0.03580.1487-0.01110.109411.39118.23129.589
60.5296-0.1312-0.06290.1804-0.16540.26350.0002-0.10610.0060.0393-0.0874-0.0026-0.3954-0.01620.05660.244-0.0001-0.02050.2078-0.0380.14379.887918.039510.5915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:6)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 7:40)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 41:82)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 83:96)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 97:131)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 132:151)A0

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