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- PDB-2a7r: Crystal structure of human Guanosine Monophosphate reductase 2 (GMPR2) -

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Basic information

Entry
Database: PDB / ID: 2a7r
TitleCrystal structure of human Guanosine Monophosphate reductase 2 (GMPR2)
ComponentsGMP reductase 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


GMP reductase / GMP reductase complex / GMP reductase activity / GMP metabolic process / Purine salvage / purine nucleobase metabolic process / metal ion binding / cytosol
Similarity search - Function
GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / GMP reductase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, J. / Wei, Z. / Zheng, M. / Gu, X. / Deng, Y. / Qiu, R. / Chen, F. / Ji, C. / Gong, W. / Xie, Y. / Mao, Y.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Human Guanosine Monophosphate Reductase 2 (GMPR2) in Complex with GMP
Authors: Li, J. / Wei, Z. / Zheng, M. / Gu, X. / Deng, Y. / Qiu, R. / Chen, F. / Ji, C. / Gong, W. / Xie, Y. / Mao, Y.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMP reductase 2
B: GMP reductase 2
C: GMP reductase 2
D: GMP reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,47615
Polymers159,6184
Non-polymers1,85811
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-207 kcal/mol
Surface area44750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.560, 110.560, 209.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
GMP reductase 2 / / Guanosine 5'-monophosphate oxidoreductase 2 / Guanosine monophosphate reductase 2


Mass: 39904.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2T1, GMP reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: sodium citrate, Li2SO4, (NH4)2SO4, pH 5.6, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 30157 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 66.3 Å2
Reflection shellResolution: 3→3.16 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
ADDREF(XTAL V. 3.0)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 227183.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2935 10 %RANDOM
Rwork0.228 ---
all0.233 30423 --
obs0.228 29287 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.621 Å2 / ksol: 0.357411 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å28.57 Å20 Å2
2--1.84 Å20 Å2
3----3.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9462 0 112 12 9586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 477 10.5 %
Rwork0.331 4064 -
obs--91.1 %

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