[English] 日本語
Yorodumi
- PDB-3wnv: Crystal structure of a glyoxylate reductase from Paecilomyes ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wnv
TitleCrystal structure of a glyoxylate reductase from Paecilomyes thermophila
Componentsglyoxylate reductase
KeywordsOXIDOREDUCTASE / Glyoxylate reductase / Paecilomyes thermophila / three-dimensional structure / cofactor specificity
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyoxylate reductase
Similarity search - Component
Biological speciesPaecilomyces sp. J18 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDuan, X. / Hu, S. / Zhou, P. / Zhou, Y. / Jiang, Z.
CitationJournal: Enzyme.Microb.Technol. / Year: 2014
Title: Characterization and crystal structure of a first fungal glyoxylate reductase from Paecilomyes thermophila
Authors: Duan, X. / Hu, S. / Zhou, P. / Zhou, Y. / Liu, Y. / Jiang, Z.
History
DepositionDec 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,0984
Polymers71,9062
Non-polymers1922
Water10,971609
1
A: glyoxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0492
Polymers35,9531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glyoxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0492
Polymers35,9531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-67 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.374, 62.763, 148.610
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein glyoxylate reductase /


Mass: 35953.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paecilomyces sp. J18 (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J185*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES buffer pH 6.5, 0.01M cobalt (II) chloride, 1.8M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 83856 / Num. obs: 82515 / % possible obs: 98.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 18.81 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13.95
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.79 / Num. unique all: 3992 / Rsym value: 0.51 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w2l

2w2l


Resolution: 1.75→49.398 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 5069 7.17 %random
Rwork0.1898 ---
obs0.1917 70659 84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→49.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 10 609 5625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145098
X-RAY DIFFRACTIONf_angle_d1.4396906
X-RAY DIFFRACTIONf_dihedral_angle_d12.5791904
X-RAY DIFFRACTIONf_chiral_restr0.098792
X-RAY DIFFRACTIONf_plane_restr0.008902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.77020.2695840.232101540
1.7702-1.7910.25371070.1977138453
1.791-1.81280.2672990.1989140354
1.8128-1.83580.24791110.1943153259
1.8358-1.85990.2281110.1942158162
1.8599-1.88540.20381340.1941165163
1.8854-1.91240.21841470.1835169967
1.9124-1.94090.25351350.1925181870
1.9409-1.97120.22921550.1936184771
1.9712-2.00360.23771520.1944196276
2.0036-2.03810.21431490.1906206579
2.0381-2.07520.22531620.193204580
2.0752-2.11510.18411660.1935226087
2.1151-2.15820.24291940.1975240090
2.1582-2.20520.20711830.1949240795
2.2052-2.25650.20322110.1933252997
2.2565-2.31290.25981980.2035254099
2.3129-2.37540.21931910.198261099
2.3754-2.44530.23382030.191253399
2.4453-2.52430.24612150.19392627100
2.5243-2.61450.22241900.1932573100
2.6145-2.71910.2311870.1973259499
2.7191-2.84290.22952150.20782621100
2.8429-2.99280.23532020.198260299
2.9928-3.18020.24722060.20592564100
3.1802-3.42570.22921750.1875260999
3.4257-3.77040.16742130.1763253297
3.7704-4.31570.17991850.1676247894
4.3157-5.43620.17511860.1677248794
5.4362-49.41810.21632030.1948262296
Refinement TLS params.Method: refined / Origin x: 7.6227 Å / Origin y: 9.9584 Å / Origin z: 37.6012 Å
111213212223313233
T-0.1983 Å2-0.011 Å20.1175 Å2-0.0021 Å20.0024 Å2---0.0446 Å2
L0.459 °2-0.062 °20.2463 °2-1.3496 °2-0.0238 °2--0.9802 °2
S0.146 Å °0.0211 Å °-0.0741 Å °-0.4471 Å °0.0013 Å °0.1612 Å °0.4886 Å °0.0462 Å °0.5069 Å °
Refinement TLS groupSelection details: all

+
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