[English] 日本語
Yorodumi
- PDB-3wyc: Structure of a meso-diaminopimelate dehydrogenase in complex with NADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wyc
TitleStructure of a meso-diaminopimelate dehydrogenase in complex with NADP
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NES / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesUreibacillus thermosphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSakuraba, H. / Akita, H. / Ohshima, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural insight into the thermostable NADP(+)-dependent meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus
Authors: Akita, H. / Seto, T. / Ohshima, T. / Sakuraba, H.
History
DepositionAug 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Meso-diaminopimelate D-dehydrogenase
B: Meso-diaminopimelate D-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6838
Polymers74,2792
Non-polymers2,4046
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-35 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.021, 123.021, 193.302
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 37139.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureibacillus thermosphaericus (bacteria)
Gene: ddh / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: G1UII1, diaminopimelate dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-NES / 2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID / TES (buffer)


Mass: 229.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15NO6S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 3.79 Å3/Da / Density % sol: 67.54 % / Mosaicity: 0.385 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: trisodium citrate dihydrate, TES, NADP, D-Lys, pH 7.5, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 66282 / Num. obs: 66282 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.084 / Χ2: 3.013 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.07-2.145.70.29666091.752100
2.14-2.235.70.24766921.943100
2.23-2.335.80.20165952.147100
2.33-2.455.70.1766572.368100
2.45-2.615.70.14166162.609100
2.61-2.815.70.11766343.044100
2.81-3.095.60.09766653.523100
3.09-3.545.50.0866274.17100
3.54-4.465.40.06766184.71100
4.46-505.50.05965694.1598.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→31.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.339 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 3365 5.1 %RANDOM
Rwork0.1734 ---
all0.1752 66282 --
obs0.1752 66282 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.75 Å2 / Biso mean: 34.372 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.36 Å20 Å2
2--0.36 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.07→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 152 387 5623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195348
X-RAY DIFFRACTIONr_bond_other_d0.0020.024978
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9867266
X-RAY DIFFRACTIONr_angle_other_deg0.938311478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9655652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37924.48250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40815864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5841532
X-RAY DIFFRACTIONr_chiral_restr0.1350.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021222
X-RAY DIFFRACTIONr_mcbond_it3.2373.1422614
X-RAY DIFFRACTIONr_mcbond_other3.2143.1412613
X-RAY DIFFRACTIONr_mcangle_it4.084.6873264
LS refinement shellResolution: 2.071→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 251 -
Rwork0.216 4630 -
all-4881 -
obs--99.84 %

+
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