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- PDB-4j7x: Crystal structure of human sepiapterin reductase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4j7x
TitleCrystal structure of human sepiapterin reductase in complex with sulfasalazine
ComponentsSepiapterin reductase
KeywordsOXIDOREDUCTASE / Reductase
Function / homology
Function and homology information


sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / tetrahydrobiopterin biosynthetic process / : / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / mitochondrion / extracellular exosome ...sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / tetrahydrobiopterin biosynthetic process / : / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / mitochondrion / extracellular exosome / nucleoplasm / cytosol
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 / DI(HYDROXYETHYL)ETHER / Chem-SAS / Sepiapterin reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGroenlund Pedersen, M. / Pojer, F. / Johnsson, K.
CitationJournal: To be Published
Title: Crystal structure of human sepiapterin reductase in complex with sulfasalazine
Authors: Groenlund Pedersen, M. / Pojer, F. / Johnsson, K.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sepiapterin reductase
B: Sepiapterin reductase
F: Sepiapterin reductase
J: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,50930
Polymers125,1604
Non-polymers6,34926
Water1,874104
1
A: Sepiapterin reductase
B: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,74815
Polymers62,5802
Non-polymers3,16813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-108 kcal/mol
Surface area19770 Å2
MethodPISA
2
F: Sepiapterin reductase
J: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,76115
Polymers62,5802
Non-polymers3,18013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-56 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.194, 149.194, 180.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.725523, 0.688189, 0.003474), (0.688195, 0.725495, 0.006676), (0.002074, 0.007235, -0.999972)-1.35551, 0.43064, 45.35485

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Components

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Protein , 1 types, 4 molecules ABFJ

#1: Protein
Sepiapterin reductase / SPR


Mass: 31290.029 Da / Num. of mol.: 4 / Fragment: Full lenght sepiapterin reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE
References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming)

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Non-polymers , 6 types, 130 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SAS / 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID / SULFASALAZINE


Mass: 398.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H14N4O5S
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 4.63 Å3/Da / Density % sol: 73.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.70 M ammonium sulphate, 0.1 M HEPES, 2 % w/v PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011
RadiationMonochromator: Si(111), Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 69669 / Num. obs: 68379 / % possible obs: 98.15 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.76 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWK

4hwk


Resolution: 2.6→48.84 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.783 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24188 3483 5 %RANDOM
Rwork0.21825 ---
all0.21945 65602 --
obs0.21945 65602 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.517 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7744 0 408 104 8256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.028278
X-RAY DIFFRACTIONr_angle_refined_deg1.1772.06211229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04251026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78324.058313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0651565
X-RAY DIFFRACTIONr_chiral_restr0.0740.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216037
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 248 -
Rwork0.322 4681 -
obs--98.3 %

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