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- PDB-4j7u: Crystal structure of human sepiapterin reductase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4j7u
TitleCrystal structure of human sepiapterin reductase in complex with sulfathiazole
ComponentsSepiapterin reductase
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / Reductase / OXIDOREDUCTASE-ANTIBIOTIC complex
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 / 4-amino-N-(1,3-thiazol-2-yl)benzenesulfonamide / Sepiapterin reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsGroenlund Pedersen, M. / Pojer, F. / Johnsson, K.
CitationJournal: Science / Year: 2013
Title: Tetrahydrobiopterin biosynthesis as an off-target of sulfa drugs.
Authors: Haruki, H. / Pedersen, M.G. / Gorska, K.I. / Pojer, F. / Johnsson, K.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
C: Sepiapterin reductase
D: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,34024
Polymers125,1604
Non-polymers5,18020
Water2,684149
1
A: Sepiapterin reductase
B: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,27613
Polymers62,5802
Non-polymers2,69611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-62 kcal/mol
Surface area19740 Å2
MethodPISA
2
C: Sepiapterin reductase
D: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,06411
Polymers62,5802
Non-polymers2,4849
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-68 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.763, 147.763, 179.503
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 5 - 250 / Label seq-ID: 35 - 280

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sepiapterin reductase / SPR


Mass: 31290.029 Da / Num. of mol.: 4
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, 169 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-YTZ / 4-amino-N-(1,3-thiazol-2-yl)benzenesulfonamide / Sulfathiazole


Mass: 255.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H9N3O2S2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / 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.: 149 / 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: 4.52 Å3/Da / Density % sol: 72.79 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2011
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 162423 / Num. obs: 161097 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.45→2.59 Å / % possible all: 95.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWK

4hwk


Resolution: 2.44→48.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.061 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22794 4077 5 %RANDOM
Rwork0.19792 ---
all0.19946 77446 --
obs0.19946 77446 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.908 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.44→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7744 0 326 149 8219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228186
X-RAY DIFFRACTIONr_angle_refined_deg1.4342.05311106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45151024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50524.103312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.805151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1441564
X-RAY DIFFRACTIONr_chiral_restr0.0850.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215952
X-RAY DIFFRACTIONr_mcbond_it0.6521.55096
X-RAY DIFFRACTIONr_mcangle_it1.29328104
X-RAY DIFFRACTIONr_scbond_it1.95233090
X-RAY DIFFRACTIONr_scangle_it3.2514.53002
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1848 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.270.5
Bmedium positional0.320.5
Cmedium positional0.290.5
Dmedium positional0.310.5
Amedium thermal1.342
Bmedium thermal0.772
Cmedium thermal0.972
Dmedium thermal1.642
LS refinement shellResolution: 2.443→2.507 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 283 -
Rwork0.274 5327 -
obs--92.62 %

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