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- PDB-3ah5: Crystal Structure of flavin dependent thymidylate synthase ThyX f... -

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Basic information

Entry
Database: PDB / ID: 3ah5
TitleCrystal Structure of flavin dependent thymidylate synthase ThyX from helicobacter pylori complexed with FAD and dUMP
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Helicobacter pylori / ThyX / FAD / dUMP
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsZhang, X. / Zhang, J. / Hu, Y. / Zou, Q. / Wang, D.
CitationJournal: To be Published
Title: Crystal structure and functional analysis of a flavin dependent thymidylate synthase from helicobacter pylori
Authors: Zhang, X. / Zhang, J. / Hu, Y. / Zou, Q. / Wang, D.
History
DepositionApr 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,69129
Polymers151,0726
Non-polymers7,61923
Water9,692538
1
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,85820
Polymers100,7154
Non-polymers5,14316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-54 kcal/mol
Surface area33440 Å2
MethodPISA
2
E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
hetero molecules

E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,66618
Polymers100,7154
Non-polymers4,95114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14370 Å2
ΔGint-53 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.920, 49.430, 143.020
Angle α, β, γ (deg.)90.000, 98.840, 90.000
Int Tables number5
Space group name H-MC121
Details4

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Components

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 25178.699 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_1533, thyX / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O26061, thymidylate synthase (FAD)
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 2.4M ammonium sulfate, 100mM HEPES pH7.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 0.97898 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.5→55.641 Å / Num. obs: 53927 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.647.60.3931.85915777960.393100
2.64-2.87.60.2952.45587773690.295100
2.8-2.997.60.2333.15276669520.233100
2.99-3.237.60.164.34907364680.16100
3.23-3.547.60.1096.14553360170.109100
3.54-3.957.60.0867.74069653840.086100
3.95-4.567.50.0728.63626848270.072100
4.56-5.597.40.0698.93038940810.069100
5.59-7.917.30.078.42337432020.07100
7.91-55.646.80.0549.81250418310.05499.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
PHASESphasing
RefinementResolution: 2.5→55.63 Å / FOM work R set: 0.837 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.246 5207 9.7 %
Rwork0.194 --
obs-53795 99.8 %
Solvent computationBsol: 48.424 Å2
Displacement parametersBiso mean: 33.858 Å2
Baniso -1Baniso -2Baniso -3
1--3.417 Å20 Å26.814 Å2
2--2.062 Å20 Å2
3---1.355 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→55.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10175 0 493 538 11206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.520.335560.28710281084
2.52-2.530.367520.3019851037
2.53-2.550.34750.2989981073
2.55-2.570.32800.25510151095
2.57-2.590.295830.249801063
2.59-2.610.3591030.279821085
2.61-2.630.281890.2439601049
2.63-2.650.364930.2739611054
2.65-2.670.311100.259461056
2.67-2.690.305960.2449531049
2.69-2.720.3091130.2399971110
2.72-2.740.2591140.2319641078
2.74-2.760.2851080.239471055
2.76-2.790.292880.2319511039
2.79-2.820.2771010.2219601061
2.82-2.840.3031140.2379731087
2.84-2.870.288950.2299561051
2.87-2.90.3281220.25310081130
2.9-2.930.3151070.2519281035
2.93-2.960.3081170.2269541071
2.96-30.321100.2249311041
3-3.030.2621210.2169651086
3.03-3.070.3081110.29831094
3.07-3.110.2931120.2379681080
3.11-3.150.312890.2189601049
3.15-3.190.26980.2199611059
3.19-3.240.2761100.2059751085
3.24-3.290.2521090.29841093
3.29-3.340.2391040.1899621066
3.34-3.390.2261090.1839391048
3.39-3.450.2531190.1889681087
3.45-3.510.2151100.1769911101
3.51-3.580.2141110.1929571068
3.58-3.650.2571120.1819381050
3.65-3.730.2481200.1859461066
3.73-3.820.2381170.17910001117
3.82-3.920.214910.179731064
3.92-4.020.2211100.1699671077
4.02-4.140.2091210.1629831104
4.14-4.270.2221060.1559441050
4.27-4.430.1691220.1349751097
4.43-4.60.2261090.1449841093
4.6-4.810.1941120.1469731085
4.81-5.070.2191030.1369891092
5.07-5.380.2011110.1679841095
5.38-5.80.2461160.1999801096
5.8-6.380.2351130.1979881101
6.38-7.30.2481080.20110021110
7.3-9.20.2990.17910221121
9.2-55.630.2041080.1799501058
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2fad.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ump.param

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