[English] 日本語
Yorodumi
- PDB-6csj: Structure of a Bacillus coagulans polyol dehydrogenase double mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6csj
TitleStructure of a Bacillus coagulans polyol dehydrogenase double mutant with an acquired D-lactate dehydrogenase activity
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / polyol dehydrogenase
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 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycerol dehydrogenase
Similarity search - Component
Biological speciesBacillus coagulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.395 Å
AuthorsHurlbert, J.C. / St.John, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5 P20 RR16461 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Kinetic characterization and structure analysis of an altered polyol dehydrogenase with d-lactate dehydrogenase activity.
Authors: Chauliac, D. / Wang, Q. / St John, F.J. / Jones, G. / Hurlbert, J.C. / Ingram, L.O. / Shanmugam, K.T.
History
DepositionMar 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
C: Glycerol dehydrogenase
D: Glycerol dehydrogenase
E: Glycerol dehydrogenase
F: Glycerol dehydrogenase
G: Glycerol dehydrogenase
H: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)314,8968
Polymers314,8968
Non-polymers00
Water9,044502
1
A: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.672, 211.772, 149.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Glycerol dehydrogenase /


Mass: 39361.973 Da / Num. of mol.: 8 / Mutation: D121N, F245S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coagulans (bacteria) / Gene: ldhA / Plasmid: pET15b / Production host: Escherichia coli Rosetta(DE3) (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A150JSL8, glycerol dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.2M Ammonium citrate dibasic, 10% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→149.71 Å / Num. obs: 126258 / % possible obs: 96.07 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / Rrim(I) all: 0.148 / Χ2: 1.105 / Net I/av σ(I): 11.641 / Net I/σ(I): 5.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6252 / CC1/2: 0.904 / Rpim(I) all: 0.21 / Rrim(I) all: 0.539 / Χ2: 0.81 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158 2016/10/03refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQ3

1kq3


Resolution: 2.395→149.71 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.208 / SU B: 10.698 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.288
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 6235 4.938 %RANDOM
Rwork0.2374 120023 --
all0.239 ---
obs-126258 96.071 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.388 Å2
Baniso -1Baniso -2Baniso -3
1--1.451 Å20 Å20 Å2
2---2.035 Å20 Å2
3---3.485 Å2
Refinement stepCycle: LAST / Resolution: 2.395→149.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22070 0 0 502 22572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01922430
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221520
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.98430384
X-RAY DIFFRACTIONr_angle_other_deg0.918350004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53952920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28525.238840
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.604153940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3241572
X-RAY DIFFRACTIONr_chiral_restr0.0720.23592
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024128
X-RAY DIFFRACTIONr_nbd_refined0.1890.28896
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1350.240142
X-RAY DIFFRACTIONr_nbtor_refined0.160.222468
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.220918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.21352
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.237
X-RAY DIFFRACTIONr_nbd_other0.1790.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2770.210
X-RAY DIFFRACTIONr_mcbond_it2.7022.52411704
X-RAY DIFFRACTIONr_mcbond_other2.7012.52411703
X-RAY DIFFRACTIONr_mcangle_it3.943.78314616
X-RAY DIFFRACTIONr_mcangle_other3.943.78314617
X-RAY DIFFRACTIONr_scbond_it3.9583.01210722
X-RAY DIFFRACTIONr_scbond_other3.9583.01210723
X-RAY DIFFRACTIONr_scangle_it5.9214.31715766
X-RAY DIFFRACTIONr_scangle_other5.9214.31715767
X-RAY DIFFRACTIONr_lrange_it6.96830.6424857
X-RAY DIFFRACTIONr_lrange_other6.9730.64224809
X-RAY DIFFRACTIONr_ncsr_local_group_10.0290.0523270
X-RAY DIFFRACTIONr_ncsr_local_group_20.0330.0523260
X-RAY DIFFRACTIONr_ncsr_local_group_30.0460.0523184
X-RAY DIFFRACTIONr_ncsr_local_group_40.030.0523306
X-RAY DIFFRACTIONr_ncsr_local_group_50.0460.0523162
X-RAY DIFFRACTIONr_ncsr_local_group_60.0470.0523128
X-RAY DIFFRACTIONr_ncsr_local_group_70.0460.0523094
X-RAY DIFFRACTIONr_ncsr_local_group_80.0310.0523250
X-RAY DIFFRACTIONr_ncsr_local_group_90.0470.0523160
X-RAY DIFFRACTIONr_ncsr_local_group_100.0360.0523260
X-RAY DIFFRACTIONr_ncsr_local_group_110.0440.0523114
X-RAY DIFFRACTIONr_ncsr_local_group_120.0470.0523164
X-RAY DIFFRACTIONr_ncsr_local_group_130.0490.0523070
X-RAY DIFFRACTIONr_ncsr_local_group_140.0440.0523162
X-RAY DIFFRACTIONr_ncsr_local_group_150.0320.0523250
X-RAY DIFFRACTIONr_ncsr_local_group_160.0420.0523098
X-RAY DIFFRACTIONr_ncsr_local_group_170.0460.0523116
X-RAY DIFFRACTIONr_ncsr_local_group_180.0430.0523050
X-RAY DIFFRACTIONr_ncsr_local_group_190.0450.0523200
X-RAY DIFFRACTIONr_ncsr_local_group_200.0310.0523276
X-RAY DIFFRACTIONr_ncsr_local_group_210.0360.0523292
X-RAY DIFFRACTIONr_ncsr_local_group_220.0270.0523320
X-RAY DIFFRACTIONr_ncsr_local_group_230.0460.0523122
X-RAY DIFFRACTIONr_ncsr_local_group_240.0480.0523172
X-RAY DIFFRACTIONr_ncsr_local_group_250.0450.0523098
X-RAY DIFFRACTIONr_ncsr_local_group_260.0330.0523260
X-RAY DIFFRACTIONr_ncsr_local_group_270.0270.0523244
X-RAY DIFFRACTIONr_ncsr_local_group_280.0360.0523194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
2.395-2.4570.3464340.31282510.313970289.51760.254
2.457-2.5240.3614850.31386610.315934997.82860.259
2.524-2.5980.3414210.29285450.294915597.93560.238
2.598-2.6770.3033620.27783750.278893197.82780.226
2.677-2.7650.2844320.26479190.265855997.56980.215
2.765-2.8620.2924430.2576960.253834397.55480.205
2.862-2.970.2853740.23874340.24802497.30810.195
2.97-3.0910.2723620.24571690.247775597.11150.207
3.091-3.2290.2993570.23768620.24744297.00350.209
3.229-3.3860.2723770.23665110.238712296.71440.213
3.386-3.5690.2422820.22662830.227680996.41650.206
3.569-3.7860.2432560.22459370.225642796.35910.208
3.786-4.0470.2262570.20755490.208605695.87190.195
4.047-4.3710.2172880.19850840.199561595.67230.189
4.371-4.7880.2432570.19947360.201523395.41370.193
4.788-5.3520.2242410.20742210.208470694.81510.198
5.352-6.1790.2591570.22838070.229419194.58360.214
6.179-7.5650.2092320.19331240.194358093.7430.188
7.565-10.6840.2051160.18324900.184280293.0050.193
10.684-149.710.3341020.28113690.284162190.74650.292

+
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