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- PDB-1oaa: MOUSE SEPIAPTERIN REDUCTASE COMPLEXED WITH NADP AND OXALOACETATE -

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Basic information

Entry
Database: PDB / ID: 1oaa
TitleMOUSE SEPIAPTERIN REDUCTASE COMPLEXED WITH NADP AND OXALOACETATE
ComponentsSEPIAPTERIN REDUCTASE
KeywordsOXIDOREDUCTASE / SEPIAPTERIN REDUCTASE / TETRAHYDROBIOPTERIN
Function / homology
Function and homology information


pteridine metabolic process / tetrahydrobiopterin metabolic process / sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) / sepiapterin reductase activity / L-phenylalanine metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / cell morphogenesis involved in neuron differentiation / voluntary musculoskeletal movement / serotonin metabolic process ...pteridine metabolic process / tetrahydrobiopterin metabolic process / sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) / sepiapterin reductase activity / L-phenylalanine metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / cell morphogenesis involved in neuron differentiation / voluntary musculoskeletal movement / serotonin metabolic process / tetrahydrobiopterin biosynthetic process / norepinephrine metabolic process / dopamine metabolic process / regulation of multicellular organism growth / protein homodimerization activity / mitochondrion
Similarity search - Function
Sepiapterin reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXALOACETATE ION / Sepiapterin reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.25 Å
AuthorsAuerbach, G. / Herrmann, A. / Bacher, A. / Huber, R.
Citation
Journal: EMBO J. / Year: 1997
Title: The 1.25 A crystal structure of sepiapterin reductase reveals its binding mode to pterins and brain neurotransmitters.
Authors: Auerbach, G. / Herrmann, A. / Gutlich, M. / Fischer, M. / Jacob, U. / Bacher, A. / Huber, R.
#1: Journal: Biol.Chem. / Year: 1997
Title: The Pathway from GTP to Tetrahydrobiopterin: Three-Dimensional Structures of GTP Cyclohydrolase I and 6-Pyruvoyl Tetrahydropterin Synthase
Authors: Auerbach, G. / Nar, H.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: 6-Pyruvoyl Tetrahydropterin Synthase, an Enzyme with a Novel Type of Active Site Involving Both Zinc Binding and an Intersubunit Catalytic Triad Motif; Site-Directed Mutagenesis of the ...Title: 6-Pyruvoyl Tetrahydropterin Synthase, an Enzyme with a Novel Type of Active Site Involving Both Zinc Binding and an Intersubunit Catalytic Triad Motif; Site-Directed Mutagenesis of the Proposed Active Center, Characterization of the Metal Binding Site and Modelling of Substrate Binding
Authors: Burgisser, D.M. / Thony, B. / Redweik, U. / Hess, D. / Heizmann, C.W. / Huber, R. / Nar, H.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Active Site Topology and Reaction Mechanism of GTP Cyclohydrolase I
Authors: Nar, H. / Huber, R. / Auerbach, G. / Fischer, M. / Hosl, C. / Ritz, H. / Bracher, A. / Meining, W. / Eberhardt, S. / Bacher, A.
#4: Journal: Structure / Year: 1995
Title: Atomic Structure of GTP Cyclohydrolase I
Authors: Nar, H. / Huber, R. / Meining, W. / Schmid, C. / Weinkauf, S. / Bacher, A.
#5: Journal: Embo J. / Year: 1994
Title: Three-Dimensional Structure of 6-Pyruvoyl Tetrahydropterin Synthase, an Enzyme Involved in Tetrahydrobiopterin Biosynthesis
Authors: Nar, H. / Huber, R. / Heizmann, C.W. / Thony, B. / Burgisser, D.
History
DepositionAug 25, 1997Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEPIAPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7155
Polymers27,6491
Non-polymers1,0674
Water8,413467
1
A: SEPIAPTERIN REDUCTASE
hetero molecules

A: SEPIAPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,43110
Polymers55,2972
Non-polymers2,1338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area7500 Å2
ΔGint-75 kcal/mol
Surface area19650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.880, 115.880, 103.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1257-

HOH

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Components

#1: Protein SEPIAPTERIN REDUCTASE /


Mass: 27648.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli)
References: UniProt: Q64105, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 3.66 Å3/Da / Density % sol: 66 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
220 mMMES1drop
31 mMdithiothreitol1drop
410 mMNADP1drop
51.5 Mammonium sulfate1reservoir
60.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→8 Å / Num. obs: 112800 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 2.9 % / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 630228
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMV. 5.23data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 1.25→6 Å / Cross valid method: FREE-R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.222 -5 %
Rwork0.2 --
obs0.2 110920 -
Refinement stepCycle: LAST / Resolution: 1.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 67 467 2469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.581
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2

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