[English] 日本語
Yorodumi
- PDB-7dsf: The Crystal Structure of human SPR from Biortus. -

+
Open data


ID or keywords:

Loading...

-
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 / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more