[English] 日本語
Yorodumi
- PDB-5gz6: Structure of D-amino acid dehydrogenase in complex with NADPH and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gz6
TitleStructure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic acid
ComponentsMeso-diaminopimelate D-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-azanyl-2-oxidanylidene-hexanoic acid / ACETATE ION / Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesUreibacillus thermosphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSakuraba, H. / Seto, T. / Hayashi, J. / Akita, H. / Yoneda, K. / Ohshima, T.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase
Authors: Hayashi, J. / Seto, T. / Akita, H. / Watanabe, M. / Hoshino, T. / Yoneda, K. / Ohshima, T. / Sakuraba, H.
History
DepositionSep 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,9057
Polymers71,7632
Non-polymers1,1425
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-63 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.838, 94.773, 138.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 35881.441 Da / Num. of mol.: 2 / Mutation: Q154L, D158G, T173I, R199M, H249N, D94A, Y224F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureibacillus thermosphaericus (bacteria)
Gene: ddh / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3) / References: UniProt: G1UII1, diaminopimelate dehydrogenase

-
Non-polymers , 5 types, 402 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-7C3 / 6-azanyl-2-oxidanylidene-hexanoic acid


Mass: 145.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.51 Å3/Da / Density % sol: 51.05 % / Mosaicity: 0.32 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2015 / Details: silicon single crystal
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 74999 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.116 / Net I/av σ(I): 34.576 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.74-1.7771.6170.4111100
1.77-1.871.2940.5391100
1.8-1.8471.1350.6121100
1.84-1.8770.9960.7141100
1.87-1.927.10.8160.8011100
1.92-1.967.10.6070.8751100
1.96-2.017.20.4580.9121100
2.01-2.067.20.4060.9371100
2.06-2.127.20.330.9531100
2.12-2.197.20.2790.9681100
2.19-2.277.20.2490.9751100
2.27-2.367.20.2150.9811100
2.36-2.477.10.1790.9841100
2.47-2.67.10.1550.9891100
2.6-2.7670.1280.9911100
2.76-2.986.90.1070.9931100
2.98-3.276.80.0870.9951100
3.27-3.756.70.0730.9951100
3.75-4.726.50.0670.994199.7
4.72-506.20.0610.994195.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZ1

5gz1


Resolution: 1.74→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.517 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3780 5 %RANDOM
Rwork0.2075 ---
obs0.2097 71112 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.43 Å2 / Biso mean: 35.261 Å2 / Biso min: 15.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.8 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 72 397 5389
Biso mean--41.29 39.35 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0195100
X-RAY DIFFRACTIONr_bond_other_d0.0030.024841
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9756906
X-RAY DIFFRACTIONr_angle_other_deg1.2153.00111142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37724.468235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15215848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7751531
X-RAY DIFFRACTIONr_chiral_restr0.1560.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215775
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021154
X-RAY DIFFRACTIONr_mcbond_it2.5782.5252537
X-RAY DIFFRACTIONr_mcbond_other2.5782.5252536
X-RAY DIFFRACTIONr_mcangle_it3.8923.7583158
LS refinement shellResolution: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 291 -
Rwork0.344 5130 -
all-5421 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37050.1284-0.0410.0749-0.14340.59550.0338-0.079-0.0117-0.0155-0.0335-0.01250.09810.0256-0.00030.03570.0050.0150.02430.0070.042414.318695.183415.4279
20.56530.0378-0.69270.0169-0.01610.9555-0.11620.1852-0.01910.01520.02540.02360.1587-0.19710.09070.0953-0.03150.03820.07130.01120.051514.42896.1934-16.2408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 48
2X-RAY DIFFRACTION1A49 - 149
3X-RAY DIFFRACTION1A150 - 256
4X-RAY DIFFRACTION1A257 - 326
5X-RAY DIFFRACTION2B2 - 74
6X-RAY DIFFRACTION2B75 - 138
7X-RAY DIFFRACTION2B139 - 256
8X-RAY DIFFRACTION2B257 - 326

+
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://pdbjlvh1.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