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- PDB-7dsf: The Crystal Structure of human SPR from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7dsf
TitleThe Crystal Structure of human SPR from Biortus.
ComponentsSepiapterin reductase
KeywordsOXIDOREDUCTASE / catalytic activity / oxidoreductase activity / acting on CH-OH group of donors
Function / homology
Function and homology information


sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Sepiapterin reductase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Sepiapterin reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, F. / Lv, Z. / Cheng, W. / Lin, D. / Meng, Q. / Zhang, B. / Huang, Y.
CitationJournal: To Be Published
Title: The Crystal Structure of human SPR from Biortus.
Authors: Wang, F. / Lv, Z. / Cheng, W. / Lin, D. / Meng, Q. / Zhang, B. / Huang, Y.
History
DepositionDec 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,9218
Polymers60,1852
Non-polymers1,7366
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-96 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.893, 74.560, 121.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sepiapterin reductase / SPR


Mass: 30092.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Production host: Escherichia coli (E. coli)
References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.01M ZnCl2, 0.1M NaAc PH5, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.065 Å / Num. obs: 47688 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2722

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I6C

6i6c


Resolution: 1.8→47.065 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.798 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2177 2289 4.808 %
Rwork0.1939 45323 -
all0.195 --
obs-47612 99.759 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.486 Å2
Baniso -1Baniso -2Baniso -3
1--1.391 Å2-0 Å20 Å2
2--1.295 Å2-0 Å2
3---0.096 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 106 247 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134077
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173922
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.6695538
X-RAY DIFFRACTIONr_angle_other_deg1.1561.5929085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31721.746189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57115703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3291532
X-RAY DIFFRACTIONr_chiral_restr0.0470.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
X-RAY DIFFRACTIONr_nbd_refined0.1810.2715
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.23553
X-RAY DIFFRACTIONr_nbtor_refined0.1360.21989
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2228
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.215
X-RAY DIFFRACTIONr_nbd_other0.1550.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.24
X-RAY DIFFRACTIONr_mcbond_it0.8892.5322084
X-RAY DIFFRACTIONr_mcbond_other0.8872.5312081
X-RAY DIFFRACTIONr_mcangle_it1.553.7932603
X-RAY DIFFRACTIONr_mcangle_other1.553.7922604
X-RAY DIFFRACTIONr_scbond_it0.9632.6611993
X-RAY DIFFRACTIONr_scbond_other0.9632.6621994
X-RAY DIFFRACTIONr_scangle_it1.6043.922934
X-RAY DIFFRACTIONr_scangle_other1.6043.922935
X-RAY DIFFRACTIONr_lrange_it3.5330.1524419
X-RAY DIFFRACTIONr_lrange_other3.44230.0094390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2921650.2673239X-RAY DIFFRACTION97.985
1.847-1.8970.2511600.2473216X-RAY DIFFRACTION99.6458
1.897-1.9520.2761960.2523090X-RAY DIFFRACTION99.6966
1.952-2.0120.2711300.2183092X-RAY DIFFRACTION100
2.012-2.0780.2451350.2092963X-RAY DIFFRACTION99.871
2.078-2.1510.2371450.2072879X-RAY DIFFRACTION99.9339
2.151-2.2320.2331370.2052757X-RAY DIFFRACTION100
2.232-2.3230.2291300.2062689X-RAY DIFFRACTION99.7523
2.323-2.4260.2111360.192555X-RAY DIFFRACTION100
2.426-2.5450.2131160.1822460X-RAY DIFFRACTION100
2.545-2.6820.1991110.1862365X-RAY DIFFRACTION99.9193
2.682-2.8440.2191130.1882205X-RAY DIFFRACTION100
2.844-3.040.2311070.1872082X-RAY DIFFRACTION100
3.04-3.2830.1981080.1841963X-RAY DIFFRACTION100
3.283-3.5960.1911030.1811795X-RAY DIFFRACTION100
3.596-4.0180.193740.1741666X-RAY DIFFRACTION100
4.018-4.6370.176760.1621472X-RAY DIFFRACTION100
4.637-5.6720.207750.1821236X-RAY DIFFRACTION99.7717
5.672-7.9890.297480.21995X-RAY DIFFRACTION99.9042
7.989-47.0650.208240.208604X-RAY DIFFRACTION99.3671

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