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- PDB-4qas: 1.27 A resolution structure of CT263-D161N (MTAN) from Chlamydia ... -

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Basic information

Entry
Database: PDB / ID: 4qas
Title1.27 A resolution structure of CT263-D161N (MTAN) from Chlamydia trachomatis
ComponentsCT263
KeywordsHYDROLASE / Chlamydia / quinones nucleosidase / futalosine pathway / substrate-bound
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 / MOLECULAR REPLACEMENT / Resolution: 1.25 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)44,7973
Polymers44,7012
Non-polymers961
Water6,341352
1
A: CT263
hetero molecules

B: CT263


Theoretical massNumber of molelcules
Total (without water)44,7973
Polymers44,7012
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x+1/2,-y+5/2,-z1
Buried area1300 Å2
ΔGint-18 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.442, 104.153, 58.148
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
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: 1.25→104.15 Å / Num. all: 110407 / Num. obs: 110407 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 16.21 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 5413 / % 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: 1.25→33.371 Å / FOM work R set: 0.8626 / SU ML: 0.14 / σ(F): 1.33 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 5516 5 %RANDOM
Rwork0.1742 ---
all0.1751 110400 --
obs0.1751 110323 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.29 Å2 / Biso mean: 27.64 Å2 / Biso min: 11.23 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 5 352 3337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093128
X-RAY DIFFRACTIONf_angle_d1.014283
X-RAY DIFFRACTIONf_chiral_restr0.076504
X-RAY DIFFRACTIONf_plane_restr0.008539
X-RAY DIFFRACTIONf_dihedral_angle_d12.0221151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.26420.31361700.293834533623100
1.2642-1.27910.32621640.291934473611100
1.2791-1.29470.30991610.272135023663100
1.2947-1.31110.30161790.266734733652100
1.3111-1.32830.28151880.258534173605100
1.3283-1.34650.24871800.253534743654100
1.3465-1.36580.2651880.251834493637100
1.3658-1.38610.29511730.241135073680100
1.3861-1.40780.27951730.231834153588100
1.4078-1.43090.19471830.227935103693100
1.4309-1.45560.22721720.222334823654100
1.4556-1.4820.2331850.20634543639100
1.482-1.51050.23282010.204634543655100
1.5105-1.54140.21952000.199634203620100
1.5414-1.57490.22021770.197534863663100
1.5749-1.61150.20472000.186334753675100
1.6115-1.65180.19751910.19434663657100
1.6518-1.69650.19311550.185634943649100
1.6965-1.74640.18711800.177434873667100
1.7464-1.80280.19471780.179834973675100
1.8028-1.86720.19531870.174235073694100
1.8672-1.94190.17931970.171134803677100
1.9419-2.03030.19491860.168934873673100
2.0303-2.13730.1721890.162335233712100
2.1373-2.27120.17841740.158435243698100
2.2712-2.44650.16051970.153534953692100
2.4465-2.69260.19961700.161535653735100
2.6926-3.0820.18521960.166635493745100
3.082-3.88210.16442010.158535953796100
3.8821-33.38250.18782210.15753720394199
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)
11.00060.09010.11881.73860.53332.8764-0.03550.109-0.0779-0.1412-0.00050.22110.2884-0.37590.02380.139-0.0498-0.01790.16290.00690.158230.6075131.7456-1.2116
22.1141.7674-1.86631.448-1.21132.46010.022-0.1898-0.07730.0583-0.21560.12530.17310.0440.190.1574-0.00720.01270.1664-0.01060.194635.424123.661416.438
32.28251.02950.08264.69920.57993.84310.0279-0.2082-0.0050.3792-0.02360.06310.1862-0.0122-0.01710.12870.0174-0.02180.1160.03430.109737.693130.339615.9836
41.33810.39250.03872.2491-0.06412.81-0.05260.0514-0.124-0.14610.06380.00360.1274-0.0212-0.00530.0742-0.0018-0.01130.12380.00710.122235.8152133.7435.7274
53.5612-1.26320.51365.33660.00663.97760.09550.1226-0.0747-0.0523-0.0015-0.0271-0.04260.0542-0.07810.0735-0.0098-0.01740.0893-0.00790.08889.6855107.484810.4774
66.21621.7518-0.6576.5613-2.34185.05240.14340.264-0.1553-0.4263-0.2349-0.09570.31970.12620.11090.14110.0297-0.00530.1573-0.01520.09825.9199103.3853.4366
77.16421.0752-3.50128.6693-5.69164.9369-0.0678-0.1311-0.35980.1076-0.3054-0.16770.12670.18370.17450.0953-0.0198-0.01770.1174-0.0170.13289.8384101.225711.079
86.5410.184-1.2345.09131.54384.552-0.2268-0.3099-0.72170.2146-0.04120.17270.9234-0.0830.26930.20260.0321-0.00140.1425-0.00950.250115.445994.786314.7642
92.5692-0.9623-1.60753.33322.24653.69470.0253-0.30540.14980.13180.0843-0.2355-0.10620.183-0.14780.11460.0024-0.01050.1316-0.01350.147219.1637112.343622.7877
105.3297-1.64650.81956.5156-1.86967.7453-0.1302-0.4337-0.24340.14790.1824-0.35230.44420.3510.04540.09430.0168-0.00970.1752-0.01620.176825.7847107.868119.6571
114.24251.2691-0.25655.70160.19784.81320.1437-0.8443-0.27370.6628-0.2205-0.17040.28850.086-0.05280.15350.0006-0.02990.2865-0.01330.149519.9111108.660430.7652
122.0531-2.36-2.25994.3563.56574.2838-0.0958-0.1478-0.06750.21360.1019-0.12470.22920.0848-0.03030.10440.0041-0.01110.1331-0.01080.151818.2767105.360722.0706
135.06320.0619-3.90232.81540.90397.6484-0.03780.24150.0684-0.19810.0294-0.1331-0.1586-0.15160.01760.10390.0111-0.00440.0827-0.01190.10699.5072115.577816.1252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 105 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 133 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 196 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 37 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 48 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 65 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 93 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 112 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 113 through 133 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 166 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 167 through 194 )B0

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