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- PDB-4qfb: 1.99 A resolution structure of SeMet-CT263 (MTAN) from Chlamydia ... -

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Basic information

Entry
Database: PDB / ID: 4qfb
Title1.99 A resolution structure of SeMet-CT263 (MTAN) from Chlamydia trachomatis
ComponentsCT263
KeywordsHYDROLASE / Chlamydia / quinones / nucleosidase / futalosine pathway
Function / homologynucleoside metabolic process / Nucleoside phosphorylase domain / Nucleoside phosphorylase superfamily / catalytic activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Nucleoside phosphorylase domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.986 Å
AuthorsBarta, M.L. / Thomas, K. / Lovell, S. / Battaile, K.P. / Schramm, V.L. / Hefty, P.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Biochemical Characterization of Chlamydia trachomatis Hypothetical Protein CT263 Supports That Menaquinone Synthesis Occurs through the Futalosine Pathway.
Authors: Barta, M.L. / Thomas, K. / Yuan, H. / Lovell, S. / Battaile, K.P. / Schramm, V.L. / Hefty, P.S.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CT263
B: CT263


Theoretical massNumber of molelcules
Total (without water)45,0782
Polymers45,0782
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CT263


Theoretical massNumber of molelcules
Total (without water)22,5391
Polymers22,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: CT263


Theoretical massNumber of molelcules
Total (without water)22,5391
Polymers22,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.853, 74.234, 78.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein CT263


Mass: 22539.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Selenomethionine derivative / Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / ATCC VR-902B / Gene: CTL0515 / Plasmid: pT7HmT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: B0B7H9, UniProt: A0A0H3MBV9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 50 mM Ammonium Sulfate, 100 mM BIS-TRIS (pH 6.4) and 32% (w/v) PEG 2K MME, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.986→47.99 Å / Num. all: 25102 / Num. obs: 24951 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 20.91 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1672 / % possible all: 95.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.986→39.03 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1880 7.96 %RANDOM
Rwork0.1665 ---
all0.17 25072 --
obs0.17 23618 94.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.88 Å2 / Biso mean: 27.5289 Å2 / Biso min: 7.13 Å2
Refinement stepCycle: LAST / Resolution: 1.986→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 0 136 3046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122985
X-RAY DIFFRACTIONf_angle_d1.1094075
X-RAY DIFFRACTIONf_chiral_restr0.054486
X-RAY DIFFRACTIONf_plane_restr0.008514
X-RAY DIFFRACTIONf_dihedral_angle_d11.6451069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9859-2.03950.27911330.21361581171491
2.0395-2.09960.2531460.19431651179794
2.0996-2.16730.24411430.16721633177694
2.1673-2.24480.21591390.16751643178293
2.2448-2.33460.23741250.16231439156483
2.3346-2.44090.21671430.15941620176393
2.4409-2.56950.21261420.16271654179694
2.5695-2.73050.18861470.16061676182395
2.7305-2.94130.24151470.16841731187897
2.9413-3.23710.20131370.16551701183895
3.2371-3.70520.2021550.16291728188397
3.7052-4.66690.18051600.141718121972100
4.6669-39.03750.20941630.18621869203298
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)
12.9223-1.31080.34486.4224-0.0782.4299-0.1419-0.331-0.17840.46210.11290.06510.1383-0.18930.03010.1207-0.02950.01460.1640.00870.11539.741259.70544.2483
21.80220.41260.15512.356-0.48762.444-0.0393-0.04060.13620.17860.0244-0.086-0.10310.02980.00470.08290.0049-0.01860.1099-0.01050.076616.195273.402542.8658
32.4391.34350.49952.46261.39120.82290.01870.09050.61610.1522-0.1263-0.426-0.30230.28850.0650.3635-0.0555-0.01470.2007-0.02830.335821.44390.609948.4966
43.2438-0.4103-0.20382.5987-0.17893.575-0.20790.27990.6157-0.04730.0035-0.2477-0.608-0.06690.04690.1655-0.0113-0.05520.1240.02560.191719.888679.846439.2339
51.73840.24990.70912.9579-0.62062.5138-0.0944-0.03220.1071-0.01080.0371-0.006-0.2504-0.14910.0270.07040.01080.00970.15220.00710.081314.349171.343237.95
62.01160.0829-0.27884.35320.97012.96010.05660.18470.0581-0.4551-0.25370.1474-0.327-0.27920.19420.14410.02540.0010.165-0.02030.16199.069849.556617.8121
72.5465-0.5333-0.69423.20920.08522.0741-0.047-0.1777-0.20220.16350.1204-0.35610.46640.1158-0.03170.17040.0166-0.03730.095-0.01870.212618.011435.495926.9131
84.19052.5244-0.78118.07170.43051.1358-0.0210.23950.0279-0.27090.4208-1.04260.13150.1042-0.42450.15110.05340.01750.1203-0.03880.278723.067535.751320.6572
91.4942-1.18640.04093.3304-0.55684.3866-0.13820.0095-0.23430.0867-0.0227-0.110.4768-0.19310.09880.1690.00210.04130.1198-0.01230.237816.057633.666321.1735
102.4977-0.84150.16496.1217-0.34313.18190.0661-0.1016-0.18410.51170.0310.45490.2659-0.1214-0.06370.1227-0.01510.00060.1351-0.04070.115512.05543.280732.0732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 48 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 93 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 102 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 133 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 194 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 65 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 93 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 112 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 162 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 163 through 194 )B0

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