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- PDB-3wb9: Crystal Structures of meso-diaminopimelate dehydrogenase from Sym... -

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Basic information

Entry
Database: PDB / ID: 3wb9
TitleCrystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum
ComponentsDiaminopimelate dehydrogenase
KeywordsOXIDOREDUCTASE / domain motion / thermo-stable / d-amino acid dehydrogenase
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 / 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 / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / 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 speciesSymbiobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsLiu, W.D. / Li, Z. / Huang, C.H. / Guo, R.T. / Wu, Q.Q. / Zhu, D.M.
CitationJournal: Chembiochem / Year: 2014
Title: Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum.
Authors: Liu, W. / Li, Z. / Huang, C.H. / Guo, R.T. / Zhao, L. / Zhang, D. / Chen, X. / Wu, Q. / Zhu, D.
History
DepositionMay 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate dehydrogenase
B: Diaminopimelate dehydrogenase
C: Diaminopimelate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,85813
Polymers99,9373
Non-polymers92110
Water20,5911143
1
A: Diaminopimelate dehydrogenase
B: Diaminopimelate dehydrogenase
C: Diaminopimelate dehydrogenase
hetero molecules

A: Diaminopimelate dehydrogenase
B: Diaminopimelate dehydrogenase
C: Diaminopimelate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,71626
Polymers199,8746
Non-polymers1,84220
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area30680 Å2
ΔGint-162 kcal/mol
Surface area65370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.249, 99.450, 80.822
Angle α, β, γ (deg.)90.000, 107.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-578-

HOH

21C-816-

HOH

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Components

#1: Protein Diaminopimelate dehydrogenase


Mass: 33312.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Symbiobacterium thermophilum (bacteria)
Strain: T / IAM 14863 / Gene: meso-dapdh, STH1425 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67PI3, diaminopimelate dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1143 / 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: 2.42 Å3/Da / Density % sol: 49.14 % / Mosaicity: 1.017 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, Glycerol, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 71273 / Num. obs: 71273 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.058 / Χ2: 2.037 / Net I/σ(I): 21.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.93-1.967.50.19834871.322197.5
1.96-28.20.18635281.476199.3
2-2.048.20.17335211.651199.4
2.04-2.088.30.15735361.928199.4
2.08-2.128.30.14635662.001199.7
2.12-2.178.40.1335522.3199.7
2.17-2.238.40.1235402.041199.8
2.23-2.298.60.10735702.016199.9
2.29-2.368.60.09535561.824199.9
2.36-2.438.70.08635681.7221100
2.43-2.528.70.07735581.5671100
2.52-2.628.70.06835841.6511100
2.62-2.748.80.06135411.6351100
2.74-2.888.80.05535781.6851100
2.88-3.068.80.0535681.7611100
3.06-3.38.80.04635742.0021100
3.3-3.638.90.04335912.3371100
3.63-4.168.90.04335822.7581100
4.16-5.248.90.04636253.2271100
5.24-508.70.04736483.5371100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIO

3bio


Resolution: 1.93→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8809 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 3566 5 %RANDOM
Rwork0.1712 ---
all-71273 --
obs-70115 98.1 %-
Solvent computationBsol: 59.7918 Å2
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 26.3739 Å2 / Biso min: 9.48 Å2
Baniso -1Baniso -2Baniso -3
1-4.621 Å20 Å2-2.61 Å2
2---2.651 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6777 0 60 1143 7980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1891.5
X-RAY DIFFRACTIONc_scbond_it2.1682
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scangle_it3.1422.5
Refine LS restraints NCSRms: 0 / Type: restrain / Weight: 300
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3gol.param

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