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- PDB-3wyb: Structure of a meso-diaminopimelate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3wyb
TitleStructure of a meso-diaminopimelate dehydrogenase
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
Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesUreibacillus thermosphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,2792
Polymers74,2792
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-46 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.747, 121.747, 194.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67 % / Mosaicity: 0.663 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Feb 9, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 41892 / Num. obs: 41892 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Χ2: 2.743 / Net I/σ(I): 17.4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.445.60.30821011.742100
2.44-2.495.70.28721171.728100
2.49-2.535.70.26820731.768100
2.53-2.595.70.2221441.795100
2.59-2.645.70.19620532.004100
2.64-2.75.70.17921142.019100
2.7-2.775.70.1520912.122100
2.77-2.855.80.13520922.25100
2.85-2.935.80.11820702.33100
2.93-3.025.80.10621142.523100
3.02-3.135.70.0920992.711100
3.13-3.265.70.08120802.926100
3.26-3.415.70.07421213.135100
3.41-3.585.60.06620973.343100
3.58-3.815.60.06420863.7100
3.81-4.15.70.06120983.584100
4.1-4.525.60.05721053.783100
4.52-5.175.70.05520913.568100
5.17-6.515.70.05520913.545100
6.51-505.30.05820554.48797.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.82 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.253 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 2117 5.1 %RANDOM
Rwork0.173 ---
all0.1752 41892 --
obs0.1752 41892 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.77 Å2 / Biso mean: 46.982 Å2 / Biso min: 23.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å21.01 Å20 Å2
2--1.01 Å2-0 Å2
3----3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 0 198 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195204
X-RAY DIFFRACTIONr_bond_other_d0.0020.024906
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.9537048
X-RAY DIFFRACTIONr_angle_other_deg0.933311300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76724.365252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5715870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5771534
X-RAY DIFFRACTIONr_chiral_restr0.1160.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
X-RAY DIFFRACTIONr_mcbond_it3.9864.3532614
X-RAY DIFFRACTIONr_mcbond_other3.9864.3512613
X-RAY DIFFRACTIONr_mcangle_it5.3646.5143264
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 165 -
Rwork0.261 2926 -
all-3091 -
obs--99.1 %

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