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- PDB-6uxc: 1.65A resolution structure of the hypothetical protein CT253 from... -

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Basic information

Entry
Database: PDB / ID: 6uxc
Title1.65A resolution structure of the hypothetical protein CT253 from Chlamydia trachomatis
ComponentsCT253
KeywordsUNKNOWN FUNCTION / CT253 / Chlamydia trachomatis
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.65 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: 1.65A resolution structure of the hypothetical protein CT253 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 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CT253
B: CT253
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7544
Polymers42,7082
Non-polymers462
Water4,774265
1
A: CT253
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3772
Polymers21,3541
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CT253
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3772
Polymers21,3541
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.187, 80.187, 114.841
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-513-

HOH

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Components

#1: Protein CT253


Mass: 21354.154 Da / Num. of mol.: 2 / Fragment: S26-S215
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: CTL0505 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3MBU8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.71 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2 M sodium formate, 0.1M Tris

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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: 1.65→44.25 Å / Num. obs: 51872 / % possible obs: 99.7 % / Redundancy: 9.4 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.2 / Num. measured all: 487014 / Scaling rejects: 4752
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.65-1.689.81.5252498925620.6471.6100
9.04-44.259.10.02434263780.99968.599.4

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.35 Å34.72 Å
Translation6.35 Å34.72 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3678refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.65→34.72 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 2426 4.83 %
Rwork0.1713 47832 -
obs0.1729 50258 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.49 Å2 / Biso mean: 37.3254 Å2 / Biso min: 19.25 Å2
Refinement stepCycle: final / Resolution: 1.65→34.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 2 265 2863
Biso mean--25.99 42.85 -
Num. residues----335
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.28181760.26932822299899
1.68-1.720.27921370.23862822295998
1.72-1.760.23631370.21992830296798
1.76-1.80.23421520.21182799295198
1.8-1.850.25531360.20282810294697
1.85-1.910.24631610.192773293497
1.91-1.970.20471120.17332821293397
1.97-2.040.1991460.165228883034100
2.04-2.120.19161550.158328883043100
2.12-2.220.19781270.151428963023100
2.22-2.330.18581250.16052752287794
2.33-2.480.21581310.16742612274390
2.48-2.670.20651450.17642748289394
2.67-2.940.21511600.182229103070100
2.94-3.370.22451320.18242716284892
3.37-4.240.1761380.14782920305898
4.24-34.720.19271560.17082825298191
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)
11.1999-0.3568-0.16570.58561.06942.16380.10540.08970.1392-0.2045-0.0096-0.1653-0.38280.1865-0.04830.3172-0.0201-0.00090.23510.02580.2764-12.734723.5033-8.3852
21.98991.0721-1.52652.9456-1.85024.1864-0.18180.0888-0.2519-0.35080.1098-0.21190.5956-0.17280.07680.3019-0.01730.01890.2115-0.01540.2836-16.359913.7332-8.0099
32.29490.8066-0.07581.33990.34030.69970.1466-0.26350.19740.1665-0.12530.0624-0.0080.0363-0.02690.3079-0.0414-0.0090.27610.00320.278-18.200625.00266.2345
41.1361-0.0365-0.18631.1406-0.17873.24310.1014-0.0507-0.0305-0.141-0.0756-0.3327-0.0520.567-0.01520.2688-0.00120.02830.27150.02820.3523-4.291221.0796-5.7169
53.90773.0290.24279.2159-0.68515.47090.0235-1.0547-0.08240.3629-0.0571-0.070.37340.47420.11320.3991-0.054-0.02980.45380.08150.2866-17.703517.497314.8398
61.17560.3896-0.68851.308-1.42754.1808-0.12220.0276-0.2282-0.38050.0188-0.31960.59640.14070.0920.3791-0.02250.08380.2247-0.0240.362-5.746117.2014-16.4703
72.43570.6672-1.88513.0449-2.53036.2791-0.1211-0.1265-0.2871-0.13-0.0709-0.44470.41540.29230.17160.32950.06420.00620.21520.00530.4078-6.903711.4326-6.7396
86.0048-0.1942.38882.3109-0.83873.17970.07030.0125-0.10520.16950.0689-0.126-0.21330.8308-0.24370.2562-0.04590.020.3627-0.02480.186-4.243546.435210.4594
95.794-1.59054.87775.6308-1.0554.12520.0296-1.24930.23960.9637-0.3825-0.7397-0.29280.38480.38410.3967-0.0766-0.04210.47560.00120.383111.476654.511214.0507
102.5138-0.45991.03741.5262-0.17040.8595-0.0661-0.20650.06130.05380.0450.1122-0.0492-0.00790.03750.2536-0.01940.00180.24580.00780.2149-7.861147.92047.8103
114.80290.3392-2.56194.6709-2.80938.7694-0.0329-0.5221-0.02870.54330.44180.42350.0602-0.6183-0.46120.2870.01680.01860.35780.05270.3147-20.737845.534610.1016
125.5170.78660.85511.6702-0.61911.40840.0659-0.41590.0861-0.0225-0.2017-0.28390.09190.18740.07920.2374-0.01510.00810.31390.04430.22151.391842.223210.6829
134.8757-4.1667-4.08855.98134.25913.7338-0.1092-0.325-0.21760.21590.5340.29391.02150.1466-0.33440.56650.14380.03580.73940.15350.753523.445236.89097.942
141.4883-0.4428-0.54760.9951-0.11311.51630.0546-0.6955-0.34350.0672-0.01690.14710.1026-0.1381-0.02040.261-0.0474-0.00330.26140.0470.2642-7.421138.73797.9999
152.69040.95230.91361.65440.07190.7177-0.1680.3170.1153-0.24080.0651-0.1185-0.05220.16390.08330.2698-0.03010.00480.32520.06220.29599.968347.40374.6221
167.12332.21832.09282.61410.62142.4981-0.14280.2387-0.0637-0.23990.0894-0.07980.04950.25830.10950.2286-0.0070.01550.2130.01550.16461.280242.187-0.402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 65 )A43 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 86 )A66 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 118 )A87 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 149 )A119 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 155 )A150 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 189 )A156 - 189
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 213 )A190 - 213
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 58 )B42 - 58
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 65 )B59 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 107 )B66 - 107
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 118 )B108 - 118
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 130 )B119 - 130
13X-RAY DIFFRACTION13chain 'B' and (resid 131 through 137 )B131 - 137
14X-RAY DIFFRACTION14chain 'B' and (resid 138 through 155 )B138 - 155
15X-RAY DIFFRACTION15chain 'B' and (resid 156 through 189 )B156 - 189
16X-RAY DIFFRACTION16chain 'B' and (resid 190 through 213 )B190 - 213

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