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- PDB-3r3j: Kinetic and structural characterization of Plasmodium falciparum ... -

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Basic information

Entry
Database: PDB / ID: 3r3j
TitleKinetic and structural characterization of Plasmodium falciparum glutamate dehydrogenase 2
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Apicoplast / Plasmodium falciparum
Function / homology
Function and homology information


apicoplast / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / nucleotide binding / cytosol
Similarity search - Function
Glutamate dehydrogenase / 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 ...Glutamate dehydrogenase / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZocher, K. / Fritz-Wolf, K. / Kehr, S. / Rahlfs, S. / Becker, K.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2012
Title: Biochemical and structural characterization of Plasmodium falciparum glutamate dehydrogenase 2.
Authors: Zocher, K. / Fritz-Wolf, K. / Kehr, S. / Fischer, M. / Rahlfs, S. / Becker, K.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 13, 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: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
D: Glutamate dehydrogenase
E: Glutamate dehydrogenase
F: Glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)307,5696
Polymers307,5696
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25840 Å2
ΔGint-58 kcal/mol
Surface area99180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.780, 140.010, 180.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutamate dehydrogenase /


Mass: 51261.422 Da / Num. of mol.: 6 / Fragment: UNP Residues 55-510 / Mutation: T161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF14_0286 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: Q8ILF7, glutamate dehydrogenase [NAD(P)+]
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS, 0.2M magnesium chloride hexahydrate, 30% PEG 4000, 0.01M spermine tetra HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. all: 64633 / Num. obs: 64381 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 42.7 Å2 / Rsym value: 0.15 / Net I/σ(I): 15.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5744 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CNS1.2refinement
XDSdata reduction
XDSdata scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMA

2bma


Resolution: 3.1→24.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5503951.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3200 5 %RANDOM
Rwork0.231 ---
obs0.231 64248 99.6 %-
all-64633 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4999 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 72 Å2
Baniso -1Baniso -2Baniso -3
1-22.19 Å20 Å20 Å2
2---4.18 Å20 Å2
3----18.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3.1→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21612 0 0 19 21631
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.442
X-RAY DIFFRACTIONc_scangle_it2.382.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 539 5.1 %
Rwork0.346 10007 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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