[English] 日本語
Yorodumi
- PDB-1vj1: Crystal structure of putative NADPH-dependent oxidoreductase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vj1
TitleCrystal structure of putative NADPH-dependent oxidoreductase from Mus musculus at 2.10 A resolution
Componentsputative NADPH-dependent oxidoreductase
KeywordsUNKNOWN FUNCTION / PUTATIVE NADPH-DEPENDENT OXIDOREDUCTASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / prostaglandin metabolic process / mitochondrion / cytosol
Similarity search - Function
Prostaglandin reductase 2 / Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Prostaglandin reductase 2 / Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Prostaglandin reductase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution
Authors: Levin, I. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Biorac, T. / Cambell, J. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / ...Authors: Levin, I. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Biorac, T. / Cambell, J. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Reyes, R. / Robb, A. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative NADPH-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)39,9741
Polymers39,9741
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.386, 91.805, 100.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein putative NADPH-dependent oxidoreductase


Mass: 39973.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ZADH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDQ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 277 K / pH: 5.1
Details: 0.1M Citrate pH 5.1, 0.2M NH4OAc, 15% PEG-4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 5.10
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
418 mg/mlprotein1drop
515 %PEG40001reservoir
60.2 Mammonium acetate1reservoir
70.1 Msodium citrate1reservoirpH5.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97950, 0.9793, 0.9567
DetectorType: ADSC / Detector: CCD / Date: May 9, 2003
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.95671
ReflectionResolution: 2.1→100.56 Å / Num. obs: 22460 / % possible obs: 95.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.59 Å2 / Rsym value: 0.069 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.431 / % possible all: 74.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50.28 Å / Num. obs: 22433 / Num. measured all: 135157 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 74.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→50.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.52 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.168
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1123 5 %RANDOM
Rwork0.18 ---
obs0.182 21310 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2---0.72 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 0 153 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222615
X-RAY DIFFRACTIONr_bond_other_d0.0010.022376
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9453540
X-RAY DIFFRACTIONr_angle_other_deg0.82435542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.50425.321109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85215442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7591510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
X-RAY DIFFRACTIONr_nbd_refined0.2010.2530
X-RAY DIFFRACTIONr_nbd_other0.1850.22528
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.36831780
X-RAY DIFFRACTIONr_mcbond_other0.5333710
X-RAY DIFFRACTIONr_mcangle_it3.25452693
X-RAY DIFFRACTIONr_scbond_it6.20581008
X-RAY DIFFRACTIONr_scangle_it7.82811846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 73
Rwork0.233 1211
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02670.3164-0.23373.53140.46151.98260.0308-0.07920.00530.2789-0.02170.0342-0.0426-0.1305-0.00910.1940.0081-0.02520.08160.02070.019717.1864.3115.423
21.3515-0.19331.08331.8092-0.06653.2123-0.0451-0.07450.03380.04930.13240.0278-0.1994-0.1416-0.08730.207-0.01210.03550.09710.05310.104519.35447.14139.4
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 13111 - 143
2X-RAY DIFFRACTION1AA315 - 351327 - 363
3X-RAY DIFFRACTION2AA132 - 314144 - 326
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.47

+
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://pdbjlvh1.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