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- PDB-4qat: 1.75 A resolution structure of CT263-D161N (MTAN) from Chlamydia ... -

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Basic information

Entry
Database: PDB / ID: 4qat
Title1.75 A resolution structure of CT263-D161N (MTAN) from Chlamydia trachomatis bound to MTA
ComponentsCT263
KeywordsHYDROLASE / Chlamydia / quinones / nucleosidase / futalosine pathway / substrate-bound
Function / homology
Function and homology information


nucleoside metabolic process / catalytic activity
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / Nucleoside phosphorylase domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 5, 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
Revision 1.3Feb 28, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CT263
B: CT263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9993
Polymers44,7012
Non-polymers2971
Water3,981221
1
A: CT263


Theoretical massNumber of molelcules
Total (without water)22,3511
Polymers22,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CT263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6482
Polymers22,3511
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.879, 104.258, 58.216
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 CT263


Mass: 22350.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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): BL21(DE3) / References: UniProt: B0B7H9, UniProt: A0A0H3MBV9*PLUS
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM ammonium sulfate, 100 mM sodium acetate trihydrate (pH 4.6) and 30% (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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→104.26 Å / Num. all: 15194 / Num. obs: 15179 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 21.98 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 15179 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
Aimlessdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-CT263

Resolution: 1.75→43.624 Å / FOM work R set: 0.8522 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 2069 5.03 %RANDOM
Rwork0.1645 ---
all0.1661 ---
obs0.1661 -99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.99 Å2 / Biso mean: 35.12 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 20 221 3214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013123
X-RAY DIFFRACTIONf_angle_d1.1034281
X-RAY DIFFRACTIONf_chiral_restr0.052504
X-RAY DIFFRACTIONf_plane_restr0.007538
X-RAY DIFFRACTIONf_dihedral_angle_d12.7491126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.79070.29261270.272325602687
1.7907-1.83550.26641300.241625732703
1.8355-1.88510.25661220.216125722694
1.8851-1.94060.27351220.197725952717
1.9406-2.00320.22311400.190825762716
2.0032-2.07480.23451270.17925702697
2.0748-2.15790.20591380.168125792717
2.1579-2.25610.20671390.16625942733
2.2561-2.3750.19351120.159326182730
2.375-2.52380.19161360.161226052741
2.5238-2.71870.22381470.16925782725
2.7187-2.99220.2151570.167726032760
2.9922-3.4250.22371410.161526422783
3.425-4.31460.1421530.135826402793
4.3146-43.63740.16141780.150227622940
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)
11.5150.2447-0.07212.411-0.18262.5213-0.06850.1884-0.1273-0.46470.11920.29970.5466-0.48920.00610.3276-0.1149-0.07270.24540.01250.237730.7304131.9399-1.0678
22.89742.1485-2.95551.2505-1.92853.2749-0.027-0.1589-0.0114-0.0145-0.18030.12370.0130.07030.26110.23-0.0111-0.00310.2082-0.01190.248435.5285123.692316.4585
32.71121.61860.23565.2650.36633.7591-0.0604-0.1514-0.2123-0.09280.00420.17220.4343-0.13650.07290.2158-0.01-0.01360.1490.04220.173835.5851127.751711.9525
42.5975-0.0954-0.26633.7760.86436.8039-0.07220.23920.0795-0.28810.0859-0.0264-0.351-0.0565-0.01050.1398-0.0561-0.04510.15850.01720.145637.2339140.24865.6089
53.91-2.08250.92985.5241-0.77162.80760.00430.07330.00040.0750.0349-0.1406-0.0780.019-0.05580.1016-0.0128-0.00870.1326-0.01250.13589.7152107.701310.5306
64.94090.25630.97496.6716-2.65723.4990.17050.2481-0.0635-0.2812-0.13240.01730.25560.20470.01260.10930.00260.02110.1679-0.02860.13877.3987103.09436.5541
72.9391-1.348-2.83092.48722.53383.5691-0.3403-0.103-0.31140.22610.08710.24591.23660.25280.18740.32230.0180.0320.21550.03610.346413.128394.029220.4877
82.0602-0.9254-0.53754.36942.22564.6201-0.0231-0.10260.02170.15750.1505-0.18910.12020.1119-0.09180.07150.01060.00130.1543-0.00490.181617.4526108.476918.6036
92.7004-0.0769-0.87993.84170.46564.7275-0.1052-0.4732-0.08690.4640.1258-0.28620.22420.2708-0.04020.17760.038-0.04280.2838-0.03590.270622.8711109.176225.5234
101.4634-1.6277-1.61993.62122.66883.1578-0.0532-0.1730.05390.13520.1758-0.28110.18250.0657-0.14450.15840.0187-0.01110.204-0.02150.219418.4625105.562822.0136
115.07620.8578-3.57123.3978-0.56382.8544-0.0890.44160.1009-0.15320.0707-0.1404-0.0767-0.61270.05810.16020.0154-0.01450.182-0.02030.16859.6064115.855515.8887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 84 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 105 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 159 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 195 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 48 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 57 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 84 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 133 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 166 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 167 through 194 )B0

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