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- PDB-6uxd: 2.0A resolution structure of the hypothetical protein CT021 from ... -

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Basic information

Entry
Database: PDB / ID: 6uxd
Title2.0A resolution structure of the hypothetical protein CT021 from Chlamydia trachomatis
ComponentsCT021
KeywordsUNKNOWN FUNCTION / CT021 / Chlamydia trachomatis
Function / homologyExported protein
Function and homology information
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2 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 General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: 2.0A resolution structure of the hypothetical protein CT021 from Chlamydia trachomatis
Authors: Barta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CT021
B: CT021


Theoretical massNumber of molelcules
Total (without water)49,3552
Polymers49,3552
Non-polymers00
Water2,918162
1
A: CT021


Theoretical massNumber of molelcules
Total (without water)24,6771
Polymers24,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CT021


Theoretical massNumber of molelcules
Total (without water)24,6771
Polymers24,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.070, 124.138, 112.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-386-

HOH

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Components

#1: Protein CT021


Mass: 24677.453 Da / Num. of mol.: 2 / Fragment: A31-F247
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: CTL0276 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3MCU1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe exact sequence of the construct may be found in Genbank, as accession/version number WP_010724988.1.

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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: 3.66 Å3/Da / Density % sol: 66.39 % / Mosaicity: 0.11 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M sodium potassium tartrate, 0.1M Tris, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.88 Å / Num. obs: 49193 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20 / Num. measured all: 330294 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2-2.056.81.0232471636120.7721.9100
8.94-46.886.30.02338776140.99974.399.1

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.62 Å38.06 Å
Translation6.62 Å38.06 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3678refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→38.06 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.06 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2392 4.87 %
Rwork0.2183 46762 -
obs0.2199 49154 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.5 Å2 / Biso mean: 51.9599 Å2 / Biso min: 26.43 Å2
Refinement stepCycle: final / Resolution: 2→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 0 162 3232
Biso mean---45.95 -
Num. residues----401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.040.29861210.311727382859
2.04-2.090.30161200.290827342854
2.09-2.130.31911380.269827292867
2.13-2.190.33051280.263427382866
2.19-2.250.31231330.253727252858
2.25-2.310.27531340.251227442878
2.31-2.390.33581490.243427092858
2.39-2.470.32971580.250727112869
2.47-2.570.2671330.251927442877
2.57-2.690.27821510.246527412892
2.69-2.830.28541520.242227232875
2.83-3.010.23661480.231327252873
3.01-3.240.26591400.22627632903
3.24-3.560.22011550.213327432898
3.56-4.080.22751390.195527882927
4.08-5.140.19161300.172928182948
5.14-38.060.24811630.210928893052

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