[English] 日本語
Yorodumi
- PDB-3uhj: Crystal structure of a probable glycerol dehydrogenase from Sinor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uhj
TitleCrystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021
ComponentsProbable glycerol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


glycerol dehydrogenase [NAD+] activity / glycerol dehydrogenase / metal ion binding
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SELENIUM ATOM / Probable glycerol dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
E: Probable glycerol dehydrogenase
F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,77424
Polymers332,5408
Non-polymers1,23416
Water9,674537
1
A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,90012
Polymers166,2704
Non-polymers6308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules

F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,87412
Polymers166,2704
Non-polymers6048
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_455x-1,y,z1
3
A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4506
Polymers83,1352
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-88 kcal/mol
Surface area24230 Å2
MethodPISA
4
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4506
Polymers83,1352
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-84 kcal/mol
Surface area24340 Å2
MethodPISA
5
E: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5167
Polymers83,1352
Non-polymers3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-94 kcal/mol
Surface area24530 Å2
MethodPISA
6
F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3585
Polymers83,1352
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-82 kcal/mol
Surface area24320 Å2
MethodPISA
7
E: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules

F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
hetero molecules

A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,77424
Polymers332,5408
Non-polymers1,23416
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area23410 Å2
ΔGint-404 kcal/mol
Surface area88280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.483, 98.996, 104.734
Angle α, β, γ (deg.)76.94, 83.38, 71.47
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Probable glycerol dehydrogenase


Mass: 41567.523 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: gldA, R02550, SMc02038 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q92MR2, glycerol dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SE / SELENIUM ATOM / Hydrogen selenide


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M NACL, 0.1M Bis-tris, 25% PEG 3350, 0.2M NDSB 221, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2011 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. all: 121795 / Num. obs: 121795 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.2
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11833 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQ3
Resolution: 2.34→45.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.435 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.395 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26358 6116 5 %RANDOM
Rwork0.19654 ---
obs0.1999 115674 98.17 %-
all-121795 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.639 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.34→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20737 0 46 537 21320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02221092
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.96728667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94752822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13122.877810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29153243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.34115181
X-RAY DIFFRACTIONr_chiral_restr0.1270.23447
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115821
X-RAY DIFFRACTIONr_mcbond_it0.8121.514055
X-RAY DIFFRACTIONr_mcangle_it1.519222349
X-RAY DIFFRACTIONr_scbond_it2.98537037
X-RAY DIFFRACTIONr_scangle_it4.6974.56318
LS refinement shellResolution: 2.341→2.402 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 402 -
Rwork0.262 8092 -
obs--93.1 %

+
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