[English] 日本語
Yorodumi
- PDB-6h07: X-ray structure of Lactobacillus brevis alcohol dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h07
TitleX-ray structure of Lactobacillus brevis alcohol dehydrogenase
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / short chain reductases/dehydrogenases / magnesium dependence / R-specific alcohol dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
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
: / R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å
AuthorsHermann, J. / Nowotny, P. / Biggel, P. / Schneider, S. / Hekmat, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP 1934 Germany
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways.
Authors: Hermann, J. / Nowotny, P. / Schrader, T.E. / Biggel, P. / Hekmat, D. / Weuster-Botz, D.
History
DepositionJul 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3914
Polymers53,3122
Non-polymers792
Water7,044391
1
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7838
Polymers106,6244
Non-polymers1584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area14480 Å2
ΔGint-100 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.030, 83.310, 114.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 26656.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: radh / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84EX5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 550 MME, Magnesium chloride, HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.482→47.15 Å / Num. all: 89189 / Num. obs: 882139 / % possible obs: 98.17 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06928 / Rpim(I) all: 0.02317 / Rrim(I) all: 0.07317 / Net I/σ(I): 17.4
Reflection shellResolution: 1.482→1.535 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.664 / Num. measured obs: 82606 / Num. unique all: 8439 / CC1/2: 0.643 / Rpim(I) all: 0.5529 / Rrim(I) all: 0.8101 / % possible all: 93.25

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSVERSION Jan 26, 2018 BUILT=20180302data reduction
XDSVERSION Jan 26, 2018 BUILT=20180302data scaling
PHASER2.8.2phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nxq

1nxq


Resolution: 1.482→47.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.455 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20304 4460 5 %RANDOM
Rwork0.18011 ---
obs0.18126 89164 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.919 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å20 Å2
2--1.3 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.482→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 2 391 4135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193844
X-RAY DIFFRACTIONr_bond_other_d0.0020.023588
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9575202
X-RAY DIFFRACTIONr_angle_other_deg1.11138348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49325.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13615658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3561516
X-RAY DIFFRACTIONr_chiral_restr0.140.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024342
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02738
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_it1.7141.9262010
X-RAY DIFFRACTIONr_mcbond_other1.7151.9262009
X-RAY DIFFRACTIONr_mcangle_it2.22.8882510
X-RAY DIFFRACTIONr_mcangle_other2.22.8882511
X-RAY DIFFRACTIONr_scbond_it2.9032.181834
X-RAY DIFFRACTIONr_scbond_other2.9062.181831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1233.1622689
X-RAY DIFFRACTIONr_long_range_B_refined4.64624.1284402
X-RAY DIFFRACTIONr_long_range_B_other4.59623.8484338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.482→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 295 -
Rwork0.355 5614 -
obs-8224 90.09 %

+
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