[English] 日本語
Yorodumi
- PDB-6g1h: Amine Dehydrogenase from Petrotoga mobilis; open form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g1h
TitleAmine Dehydrogenase from Petrotoga mobilis; open form
ComponentsDihydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / amine dehydrogenase / reductive aminase / NADH
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrodipicolinate reductase
Similarity search - Component
Biological speciesPetrotoga mobilis SJ95 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsBeloti, L. / Frese, A. / Mayol, O. / Vergne-Vaxelaire, C. / Grogan, G.
CitationJournal: Nat Catal / Year: 2019
Title: A family of native amine dehydrogenases for the asymmetric reductive amination of ketones
Authors: Mayol, O. / Bastard, K. / Beloti, L. / Frese, A. / Turkenburg, J.P. / Petit, J.-L. / Mariage, A. / Debard, A. / Pellouin, V. / Perret, A. / de Berardinis, V. / Zaparucha, A. / Grogan, G. / Vergne-Vaxelaire, C.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4945
Polymers37,6451
Non-polymers8504
Water5,477304
1
A: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,98910
Polymers75,2892
Non-polymers1,6998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7160 Å2
ΔGint-20 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.038, 82.038, 217.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Dihydrodipicolinate reductase


Mass: 37644.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petrotoga mobilis SJ95 (bacteria) / Gene: Pmob_1166 / Production host: Escherichia coli (E. coli) / References: UniProt: A9BHL2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-tris pH 6.5 0.8M Li2SO4

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.79→71.04 Å / Num. obs: 41623 / % possible obs: 99.2 % / Redundancy: 23.6 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Net I/σ(I): 34.7
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2379 / CC1/2: 0.99 / Rpim(I) all: 0.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→71.04 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.054 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19617 2032 4.9 %RANDOM
Rwork0.15866 ---
obs0.16051 39218 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.508 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å20 Å2
2--1.16 Å20 Å2
3----3.76 Å2
Refinement stepCycle: 1 / Resolution: 1.79→71.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 56 305 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192737
X-RAY DIFFRACTIONr_bond_other_d0.0020.022616
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.9933727
X-RAY DIFFRACTIONr_angle_other_deg1.08936099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.76325.825103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.215476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.719158
X-RAY DIFFRACTIONr_chiral_restr0.1360.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02477
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_it2.6262.7971382
X-RAY DIFFRACTIONr_mcbond_other2.6272.7961381
X-RAY DIFFRACTIONr_mcangle_it3.2044.1741726
X-RAY DIFFRACTIONr_mcangle_other3.2034.1751727
X-RAY DIFFRACTIONr_scbond_it4.2573.2371355
X-RAY DIFFRACTIONr_scbond_other4.2473.2371355
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0424.6811995
X-RAY DIFFRACTIONr_long_range_B_refined7.02735.5143092
X-RAY DIFFRACTIONr_long_range_B_other7.02835.5293093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 143 -
Rwork0.22 2779 -
obs--97.66 %

+
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