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- PDB-2bma: The crystal structure of Plasmodium falciparum glutamate dehydrog... -

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Basic information

Entry
Database: PDB / ID: 2bma
TitleThe crystal structure of Plasmodium falciparum glutamate dehydrogenase, a putative target for novel antimalarial drugs
ComponentsGLUTAMATE DEHYDROGENASE (NADP+)
KeywordsOXIDOREDUCTASE / PLASMODIUM FALCIPARUM / MALARIA / GLUTAMATE DEHYDROGENASE / DRUG DESIGN / CRYSTAL STRUCTURE ANALYSIS / OLIGOMER ORGANIZATION / NADP
Function / homology
Function and homology information


glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / nucleotide binding
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: 2.7 Å
AuthorsWerner, C. / Stubbs, M.T. / Krauth-Siege, R.L. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Plasmodium Falciparum Glutamate Dehydrogenase, a Putative Target for Novel Antimalarial Drugs
Authors: Werner, C. / Stubbs, M.T. / Krauth-Siege, R.L. / Klebe, G.
History
DepositionMar 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE DEHYDROGENASE (NADP+)
B: GLUTAMATE DEHYDROGENASE (NADP+)
C: GLUTAMATE DEHYDROGENASE (NADP+)
D: GLUTAMATE DEHYDROGENASE (NADP+)
E: GLUTAMATE DEHYDROGENASE (NADP+)
F: GLUTAMATE DEHYDROGENASE (NADP+)


Theoretical massNumber of molelcules
Total (without water)315,4616
Polymers315,4616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)167.612, 96.851, 196.192
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GLUTAMATE DEHYDROGENASE (NADP+)


Mass: 52576.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O96940, glutamate dehydrogenase (NADP+)

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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: 2.58 Å3/Da / Density % sol: 51.88 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 82010 / % possible obs: 93.3 % / Observed criterion σ(I): 3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.4 / % possible all: 84.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BGV

1bgv


Resolution: 2.7→100 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 7880 9.1 %RANDOM
Rwork0.2489 ---
obs0.2489 78843 91.2 %-
Solvent computationBsol: 19.1561 Å2 / ksol: 0.331558 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.617 Å20 Å2-1.124 Å2
2---2.884 Å20 Å2
3---0.267 Å2
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22068 0 0 0 22068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0088
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM

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