[English] 日本語
Yorodumi
- PDB-4jig: Crystal structure of a putative dehydrogenase from Burkholderia c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jig
TitleCrystal structure of a putative dehydrogenase from Burkholderia cenocepacia
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Disease / NADP-dependent
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative dehydrogenase from Burkholderia cenocepacia
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0514
Polymers26,8411
Non-polymers2103
Water2,738152
1
A: Dehydrogenase
hetero molecules

A: Dehydrogenase
hetero molecules

A: Dehydrogenase
hetero molecules

A: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,20616
Polymers107,3654
Non-polymers84112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area14250 Å2
ΔGint-75 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.890, 102.810, 123.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

-
Components

#1: Protein Dehydrogenase


Mass: 26841.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BCAL2369, BceJ2315_23290 / Plasmid: pBG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E5P7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: BuceA.00010.a.B1 PS01733 at 22.8 mg/mL against JCSG+ screen condition D11, 140 mM CaCl2, 70 mM NaOAc pH 4.6, 14% isopropanol, 30% glycerol, crystal tracking ID 242030d11, unique puck ID smk5- ...Details: BuceA.00010.a.B1 PS01733 at 22.8 mg/mL against JCSG+ screen condition D11, 140 mM CaCl2, 70 mM NaOAc pH 4.6, 14% isopropanol, 30% glycerol, crystal tracking ID 242030d11, unique puck ID smk5-3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 20185 / Num. obs: 20122 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 27.516 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.4953.326566146199.5
1.9-1.950.4193.796448144699.7
1.95-2.010.3025.396232138699.6
2.01-2.070.2576.146044134999.9
2.07-2.140.217.55870130899.7
2.14-2.210.1579.975748127799.9
2.21-2.290.13411.275520123599.9
2.29-2.390.11512.715364119699.8
2.39-2.490.10314.2650891136100
2.49-2.620.08317.34918108899.9
2.62-2.760.06819.894754105799.9
2.76-2.930.05624.024319965100
2.93-3.130.04528.874204938100
3.13-3.380.03634.923864870100
3.38-3.70.02743.23353881199.8
3.7-4.140.02450.943127718100
4.14-4.780.0256.52281065799.4
4.78-5.850.02153.192442550100
5.85-8.270.01957.53189743799.5
8.270.01668.9895323790.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.74 Å
Translation3 Å19.74 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IQG

4iqg


Resolution: 1.85→19.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1733 / WRfactor Rwork: 0.1336 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8819 / SU B: 5.331 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1131 / SU Rfree: 0.1168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 1021 5.1 %RANDOM
Rwork0.1503 ---
obs0.1526 20060 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.48 Å2 / Biso mean: 25.6368 Å2 / Biso min: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å2-0 Å2
2---1.59 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 14 152 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191717
X-RAY DIFFRACTIONr_bond_other_d0.0010.021669
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9712334
X-RAY DIFFRACTIONr_angle_other_deg0.83533794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0922.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18115251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_mcbond_it1.3791.98954
X-RAY DIFFRACTIONr_mcbond_other1.3491.977951
X-RAY DIFFRACTIONr_mcangle_it2.0222.9521188
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 92 -
Rwork0.182 1297 -
all-1389 -
obs--95.79 %
Refinement TLS params.Method: refined / Origin x: 19.7661 Å / Origin y: 10.3567 Å / Origin z: 15.4962 Å
111213212223313233
T0.0439 Å2-0.0205 Å20.0214 Å2-0.032 Å2-0.0138 Å2--0.0252 Å2
L0.1255 °2-0.0444 °2-0.0756 °2-0.3228 °20.0657 °2--0.2799 °2
S-0.0456 Å °0.043 Å °-0.009 Å °-0.0248 Å °0.0226 Å °0.0036 Å °0.0775 Å °0.0128 Å °0.0229 Å °

+
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