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- PDB-3k92: Crystal structure of a E93K mutant of the majour Bacillus subtili... -

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Basic information

Entry
Database: PDB / ID: 3k92
TitleCrystal structure of a E93K mutant of the majour Bacillus subtilis glutamate dehydrogenase RocG
ComponentsNAD-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / RocG / glutamate dehydrogenase / NAD
Function / homology
Function and homology information


glutamate dehydrogenase / glutamate catabolic process / : / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1210 / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ...Helicase, Ruva Protein; domain 3 - #1210 / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Helicase, Ruva Protein; domain 3 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Catabolic NAD-specific glutamate dehydrogenase RocG
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsGunka, K. / Newman, J.A. / Commichau, F.M. / Herzberg, C. / Rodrigues, C. / Hewitt, L. / Lewis, R.J. / Stulke, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties
Authors: Gunka, K. / Newman, J.A. / Commichau, F.M. / Herzberg, C. / Rodrigues, C. / Hewitt, L. / Lewis, R.J. / Stulke, J.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 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

Downloads & links

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Assembly

Deposited unit
A: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase
C: NAD-specific glutamate dehydrogenase
D: NAD-specific glutamate dehydrogenase
E: NAD-specific glutamate dehydrogenase
F: NAD-specific glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,67911
Polymers280,1486
Non-polymers5315
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-26 kcal/mol
Surface area86530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.614, 143.072, 162.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NAD-specific glutamate dehydrogenase / NAD-GDH


Mass: 46691.383 Da / Num. of mol.: 6 / Mutation: E93K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P39633, glutamate dehydrogenase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 824 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE UNIPROTKB/SWISS-PROT P39633 (DHE2_BACSU). ...THE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE UNIPROTKB/SWISS-PROT P39633 (DHE2_BACSU). A324R IS SEQUENCE CONFLICT OF DHE2_BACSU.

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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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% Peg 3350, 20% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 142264 / Num. obs: 142264 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→18.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.852 / SU B: 5.978 / SU ML: 0.147 / SU R Cruickshank DPI: 0.252 / SU Rfree: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 7159 5 %RANDOM
Rwork0.182 ---
all0.185 141980 --
obs0.185 141980 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 124.86 Å2 / Biso mean: 52.894 Å2 / Biso min: 19.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→18.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18769 0 35 824 19628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02219145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213107
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.96525873
X-RAY DIFFRACTIONr_angle_other_deg1.112331998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75452424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10824.235817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.629153362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.73715124
X-RAY DIFFRACTIONr_chiral_restr0.1250.22894
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02121299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023759
X-RAY DIFFRACTIONr_mcbond_it0.8911.512033
X-RAY DIFFRACTIONr_mcbond_other0.2311.54989
X-RAY DIFFRACTIONr_mcangle_it1.655219374
X-RAY DIFFRACTIONr_scbond_it2.80537112
X-RAY DIFFRACTIONr_scangle_it4.4254.56499
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 516 -
Rwork0.231 9754 -
all-10270 -
obs--99.9 %

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