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- PDB-3wgo: Crystal structure of Q154L/T173I/R199M/P248S/H249/N276S mutant of... -

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Basic information

Entry
Database: PDB / ID: 3wgo
TitleCrystal structure of Q154L/T173I/R199M/P248S/H249/N276S mutant of meso-dapdh from Clostridium tetani E88
ComponentsMeso-diaminopimelate dehydrogenase
KeywordsOXIDOREDUCTASE / meso-diaminopimelate dehydrogenase / mutation / domain motion
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
Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 Q154L/T173I/R199M/P248S/H249 mutant of meso-dapdh from Clostridium tetani E88
Authors: Liu, W.D. / Li, Z. / Huang, C.H. / Guo, R.T. / Wu, Q.Q. / Zhu, D.M.
History
DepositionAug 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,5672
Polymers72,5672
Non-polymers00
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-34 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.130, 135.619, 60.670
Angle α, β, γ (deg.)90.00, 110.46, 90.00
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.45 Å3/Da / Density % sol: 49.74 % / Mosaicity: 0.331 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG20000, MES, glycerol, 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: 2.05→25 Å / Num. all: 44540 / Num. obs: 44540 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Χ2: 1.56 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.123.80.50944321.2971100
2.12-2.213.80.36944281.3581100
2.21-2.313.80.29144661.3931100
2.31-2.433.90.20644441.3351100
2.43-2.583.90.1644211.4761100
2.58-2.783.80.1244801.761199.9
2.78-3.063.90.08744431.9081100
3.06-3.53.90.0544461.6161100
3.5-4.413.80.0444692.224199.4
4.41-253.90.02545111.238199.8

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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-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F06

1f06


Resolution: 2.05→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8031 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2595 2119 4.7 %
Rwork0.1985 --
all-42319 -
obs-42317 94.8 %
Solvent computationBsol: 73.8875 Å2
Displacement parametersBiso max: 96.76 Å2 / Biso mean: 41.8894 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1-7.995 Å20 Å2-1.283 Å2
2---12.525 Å2-0 Å2
3---4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 0 781 5837
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.343
X-RAY DIFFRACTIONc_mcbond_it1.6071.5
X-RAY DIFFRACTIONc_scbond_it2.1782
X-RAY DIFFRACTIONc_mcangle_it2.5862
X-RAY DIFFRACTIONc_scangle_it3.1592.5
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 (%)
2.05-2.120.37471790.29033544372383.6
2.12-2.210.27472040.25283777398189.5
2.21-2.310.31391900.24113898408891.6
2.31-2.430.32392180.23963971418994.2
2.43-2.580.29872050.23684016422195.3
2.58-2.780.32572080.23234164437297.5
2.78-3.060.30332350.22474144437998.1
3.06-3.50.25832450.19344169441499.2
3.5-4.410.22242390.17164209444899
4.41-250.20451960.15954306450299.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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