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- PDB-3wgy: Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N27... -

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Basic information

Entry
Database: PDB / ID: 3wgy
TitleCrystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with 4-methyl-2-oxovalerate of from Clostridium tetani E88
ComponentsMeso-diaminopimelate dehydrogenase
KeywordsOXIDOREDUCTASE / meso-diaminopimelate dehydrogenase / mutation / domain motion / 4-methyl-2-oxovalerate
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 / 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-OXO-4-METHYLPENTANOIC ACID / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLiu, W.D. / Li, Z. / Huang, C.H. / Guo, R.T. / Wu, Q.Q. / Zhu, D.M.
CitationJournal: to be published
Title: Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with 4-methyl-2-oxovalerate of from Clostridium tetani E88
Authors: Liu, W.D. / Li, Z. / Huang, C.H. / Guo, R.T. / Wu, Q.Q. / Zhu, D.M.
History
DepositionAug 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 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 1.2Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,6973
Polymers72,5672
Non-polymers1301
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-30 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.191, 135.536, 60.792
Angle α, β, γ (deg.)90.000, 110.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Meso-diaminopimelate dehydrogenase


Mass: 36283.250 Da / Num. of mol.: 2 / Mutation: Q154L, T173I, R199M, P248S, H249N, N276S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani (bacteria) / Strain: E88 / Gene: CTC_02532, meso-dapdh / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q890V3, diaminopimelate dehydrogenase
#2: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.51 Å3/Da / Density % sol: 50.97 % / Mosaicity: 0.324 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG20000, MES, glycerol, 4-methyl-2-oxovalerate, pH 6.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 48131 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.042 / Χ2: 1.616 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.074.60.43848121.49199.9
2.07-2.154.70.30748261.5131100
2.15-2.254.70.2347901.5431100
2.25-2.374.70.16447801.5071100
2.37-2.524.70.11548051.5181100
2.52-2.714.70.08448051.791100
2.71-2.994.70.06448171.9741100
2.99-3.424.70.03748091.5081100
3.42-4.34.60.03548302.21100
4.3-254.70.02248571.142199.5

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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 / Resolution: 2→24.4 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7916 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2639 2294 4.8 %
Rwork0.2046 --
obs-46040 95.5 %
Solvent computationBsol: 68.8785 Å2
Displacement parametersBiso max: 107.41 Å2 / Biso mean: 45.6785 Å2 / Biso min: 17.89 Å2
Baniso -1Baniso -2Baniso -3
1-9.69 Å20 Å20.334 Å2
2---13.241 Å2-0 Å2
3---3.55 Å2
Refinement stepCycle: LAST / Resolution: 2→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 9 896 5961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.455
X-RAY DIFFRACTIONc_mcbond_it1.5761.5
X-RAY DIFFRACTIONc_scbond_it2.0792
X-RAY DIFFRACTIONc_mcangle_it2.5562
X-RAY DIFFRACTIONc_scangle_it2.9882.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.070.321970.28783918411585.4
2.07-2.150.31012440.25424140438490.7
2.15-2.250.35022160.26274247446393
2.25-2.370.33522130.25024303451694.3
2.37-2.520.3422270.25634419464696.7
2.52-2.710.31732340.24664475470997.8
2.71-2.990.3082370.22994528476598.8
2.99-3.420.31072400.21224546478699.4
3.42-4.310.21942510.17254578482999.9
4.31-500.010.2022350.16914592482799
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3COI.param

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