[English] 日本語
Yorodumi
- PDB-4bmn: apo structure of short-chain alcohol dehydrogenase from Ralstonia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bmn
Titleapo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428
ComponentsALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
KeywordsOXIDOREDUCTASE / KRED / BIOCATALYST
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function
: / PKS_KR / 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
Alclohol dehydrogenase/short-chain dehydrogenase
Similarity search - Component
Biological speciesRALSTONIA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMan, H. / Kulig, J. / Rother, D. / Grogan, G.
CitationJournal: Top.Catal. / Year: 2014
Title: Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium Spp. Reveal the Molecular Basis for Their Recognition of 'Bulky-Bulky' Ketones
Authors: Man, H. / Kedziora, K. / Kulig, J. / Frank, A. / Lavandera, I. / Gotor-Fernandez, V. / Rother, D. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionMay 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
B: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
C: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
D: ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,11913
Polymers108,4594
Non-polymers6609
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-68.5 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.480, 52.510, 151.470
Angle α, β, γ (deg.)90.00, 116.57, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7713, -0.5759, 0.271), (-0.5692, 0.4336, -0.6986), (0.2848, -0.6931, -0.6622)38.07, 40.76, 52.76
2given(-0.9587, 0.1399, 0.2478), (0.1347, -0.5438, 0.8283), (0.2506, 0.8274, 0.5025)39.64, -23, 6.105
3given(0.7291, 0.4375, -0.5268), (0.4375, -0.8895, -0.1322), (-0.5264, -0.1341, -0.8396)22.15, 3.724, 75.96

-
Components

#1: Protein
ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE / ALCOHOL DEHYDROGENASE


Mass: 27114.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SP. (bacteria) / Strain: DSMZ 6428 / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0IR58, alcohol dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Sequence details'QGPA' AT THE BEGINNING ARE PART OF A LINKING SEQUENCE TO AN N-TERMINAL HIS-TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 7
Details: 0.1M BIS-TRIS PROPANE PH 7.0 CONTAINING 20% (W/V) PEG 3350 AND 0.02 M SODIUM-POTASSIUM PHOSPHATE. THE PROTEIN CONCENTRATION WAS 24 MG ML-1.

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.52→60.86 Å / Num. obs: 149646 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.6
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.9 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FGS

4fgs


Resolution: 1.5→60.86 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.26 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18784 7501 5 %RANDOM
Rwork0.15812 ---
obs0.15962 141654 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.997 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.12 Å2
2--1.87 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6877 0 43 847 7767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0197071
X-RAY DIFFRACTIONr_bond_other_d0.0110.027024
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9749589
X-RAY DIFFRACTIONr_angle_other_deg1.683316015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7122.804271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.088151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3061565
X-RAY DIFFRACTIONr_chiral_restr0.1310.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028073
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1241.9793750
X-RAY DIFFRACTIONr_mcbond_other2.1231.9793748
X-RAY DIFFRACTIONr_mcangle_it2.882.9624686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0912.263321
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 561 -
Rwork0.213 10230 -
obs--95.97 %

+
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