[English] 日本語
Yorodumi
- PDB-8hp0: Crystal structure of meso-diaminopimelate dehydrogenase from Prev... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hp0
TitleCrystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / asymmetric unit / C221 / fold
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesPrevotella timonensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsTan, Y. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Environ.Microbiol. / Year: 2023
Title: Rational Design of Meso -Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d- p -Hydroxyphenylglycine.
Authors: Tan, Y. / Gao, C. / Song, W. / Wei, W. / Liu, J. / Gao, C. / Guo, L. / Chen, X. / Liu, L. / Wu, J.
History
DepositionDec 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Meso-diaminopimelate D-dehydrogenase
B: Meso-diaminopimelate D-dehydrogenase
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,23714
Polymers97,7533
Non-polymers1,48311
Water2,918162
1
A: Meso-diaminopimelate D-dehydrogenase
B: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1269
Polymers65,1692
Non-polymers9577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-82 kcal/mol
Surface area25610 Å2
MethodPISA
2
C: Meso-diaminopimelate D-dehydrogenase
hetero molecules

C: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,22210
Polymers65,1692
Non-polymers1,0538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7540 Å2
ΔGint-98 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.750, 190.470, 101.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Meso-diaminopimelate D-dehydrogenase / DAPDH / Meso-DAP dehydrogenase


Mass: 32584.482 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella timonensis (bacteria) / Gene: BFS16_11360 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2K0XCZ3, diaminopimelate dehydrogenase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, and 0.1 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 28, 2022 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.47→44.87 Å / Num. obs: 35517 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.3
Reflection shellResolution: 2.47→2.57 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.507 / Num. unique obs: 3948 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→44.91 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.393 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.638 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26561 1818 5.1 %RANDOM
Rwork0.22414 ---
obs0.22624 33818 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.692 Å2
Baniso -1Baniso -2Baniso -3
1--3.18 Å2-0 Å20 Å2
2--0.31 Å2-0 Å2
3---2.86 Å2
Refinement stepCycle: 1 / Resolution: 2.47→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 85 162 7051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137026
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156794
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.6369513
X-RAY DIFFRACTIONr_angle_other_deg1.1181.57815708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1885899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66322.809324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.634151243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9291539
X-RAY DIFFRACTIONr_chiral_restr0.0480.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021421
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_it1.9714.3353581
X-RAY DIFFRACTIONr_mcbond_other1.9714.3353580
X-RAY DIFFRACTIONr_mcangle_it3.1996.4984473
X-RAY DIFFRACTIONr_mcangle_other3.1996.4984474
X-RAY DIFFRACTIONr_scbond_it2.0094.5923445
X-RAY DIFFRACTIONr_scbond_other1.9924.5663411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3836.7434989
X-RAY DIFFRACTIONr_long_range_B_refined5.29250.3217178
X-RAY DIFFRACTIONr_long_range_B_other5.24450.3167159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A9073
12B9073
21A9035
22C9035
31B9030
32C9030
LS refinement shellResolution: 2.47→2.53 Å
RfactorNum. reflection% reflection
Rfree0.368 148 -
Rwork0.346 2421 -
obs--99.23 %

+
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