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- PDB-3wbf: Crystal Structure of meso-diaminopimelate dehydrogenase from Symb... -

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Basic information

Entry
Database: PDB / ID: 3wbf
TitleCrystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP
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
2,6-DIAMINOPIMELIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesSymbiobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 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 15, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)104,21225
Polymers99,9373
Non-polymers4,27422
Water25,3291406
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)208,42350
Polymers199,8746
Non-polymers8,54944
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area41220 Å2
ΔGint-142 kcal/mol
Surface area61870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.351, 99.687, 67.172
Angle α, β, γ (deg.)90.00, 108.52, 90.00
Int Tables number5
Space group name H-MC121

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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-API / 2,6-DIAMINOPIMELIC ACID / Diaminopimelic acid


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H14N2O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1406 / 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: 2.74 Å3/Da / Density % sol: 55.07 % / Mosaicity: 0.932 °
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, PEG 6000, NADP+, DAP,, pH 7.5, vapor diffusion, sitting drop, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 61605 / Num. obs: 61060 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Χ2: 1.324 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.12-2.23.60.32557301.09193.9
2.2-2.283.70.31261201.153199.8
2.28-2.393.70.25161221.167199.9
2.39-2.513.70.22361301.209199.9
2.51-2.673.70.17161461.244199.8
2.67-2.883.60.14261461.375199.8
2.88-3.173.60.11261171.498199.8
3.17-3.623.50.07561421.513199.6
3.62-4.563.40.06161821.513199.6
4.56-303.40.05762251.509199.4

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIO

3bio


Resolution: 2.12→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8134 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 2910 4.8 %RANDOM
Rwork0.1983 ---
all-61060 --
obs-57533 94.2 %-
Solvent computationBsol: 60.4694 Å2
Displacement parametersBiso max: 88.05 Å2 / Biso mean: 29.0927 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1--11.66 Å20 Å20.541 Å2
2---7.709 Å2-0 Å2
3---19.369 Å2
Refinement stepCycle: LAST / Resolution: 2.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6777 0 279 1406 8462
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2311.5
X-RAY DIFFRACTIONc_scbond_it2.0552
X-RAY DIFFRACTIONc_mcangle_it1.8252
X-RAY DIFFRACTIONc_scangle_it2.8492.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3gol.param
X-RAY DIFFRACTION4NAP.param
X-RAY DIFFRACTION5api.param

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