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- PDB-2b4t: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 2b4t
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom resolution reveals intriguing extra electron density in the active site
Componentsglyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / GAPDH / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding 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
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRobien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site
Authors: Robien, M.A. / Bosch, J. / Buckner, F.S. / Van Voorhis, W.C. / Worthey, E.A. / Myler, P. / Mehlin, C. / Boni, E.E. / Kalyuzhniy, O. / Anderson, L. / Lauricella, A. / Gulde, S. / Luft, J.R. / ...Authors: Robien, M.A. / Bosch, J. / Buckner, F.S. / Van Voorhis, W.C. / Worthey, E.A. / Myler, P. / Mehlin, C. / Boni, E.E. / Kalyuzhniy, O. / Anderson, L. / Lauricella, A. / Gulde, S. / Luft, J.R. / Detitta, G. / Caruthers, J.M. / Hodgson, K.O. / Soltis, M. / Zucker, F. / Verlinde, C.L. / Merritt, E.A. / Schoenfeld, L.W. / Hol, W.G.
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: glyceraldehyde-3-phosphate dehydrogenase
P: glyceraldehyde-3-phosphate dehydrogenase
Q: glyceraldehyde-3-phosphate dehydrogenase
R: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,84011
Polymers150,5774
Non-polymers3,2637
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21080 Å2
ΔGint-127 kcal/mol
Surface area44840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.687, 106.056, 91.057
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 37644.266 Da / Num. of mol.: 4 / Mutation: V3A, N336T, N337S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF14_0598 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)
References: UniProt: Q8T6B1, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF / AEBSF


Mass: 203.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 3350; 200 MILLIMOLAR NA F; 100 MILLIMOLAR BIS-TRIS-PROPANE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9807
SYNCHROTRONSSRL BL9-220.9807
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 4, 2005double crystal
QUANTUM 3152CCDMar 4, 2005double crystal
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 2.5→46.625 Å / Num. all: 42843 / Num. obs: 42843 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 68.4 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 6197 / Rsym value: 0.484 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1J0X

1j0x


Resolution: 2.5→43.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 19.138 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21677 2147 5 %RANDOM
Rwork0.17352 ---
all0.17575 40675 --
obs0.17575 40675 97.69 %-
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 mean: 48.808 Å2
Baniso -1Baniso -2Baniso -3
1-4.22 Å20 Å21.59 Å2
2---1.07 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10184 0 215 232 10631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210391
X-RAY DIFFRACTIONr_bond_other_d0.0010.029431
X-RAY DIFFRACTIONr_angle_refined_deg1.081.97914169
X-RAY DIFFRACTIONr_angle_other_deg0.712321800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97324.307397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.659151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.911543
X-RAY DIFFRACTIONr_chiral_restr0.0590.21645
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022004
X-RAY DIFFRACTIONr_nbd_refined0.1870.22017
X-RAY DIFFRACTIONr_nbd_other0.1690.29657
X-RAY DIFFRACTIONr_nbtor_refined0.1730.25050
X-RAY DIFFRACTIONr_nbtor_other0.080.25994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2412
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.25748476
X-RAY DIFFRACTIONr_mcbond_other0.24942732
X-RAY DIFFRACTIONr_mcangle_it1.647610589
X-RAY DIFFRACTIONr_scbond_it1.92464395
X-RAY DIFFRACTIONr_scangle_it2.797103580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.635 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.389 309 -
Rwork0.322 5882 -
obs--97.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78870.1285-0.35851.73880.13811.82520.17670.17350.6462-0.3289-0.0749-0.2672-0.29080.1274-0.1018-0.20820.0406-0.0005-0.10430.08340.134124.18214.887.766
21.1882-0.2843-0.03992.80130.54112.2330.00810.1772-0.2349-0.0407-0.22370.40880.5806-0.23550.2155-0.114-0.045-0.0823-0.0881-0.0994-0.02364.295-17.328.987
32.5014-0.8575-0.46421.77160.23691.0893-0.2186-0.6030.11380.61740.1441-0.35470.33330.29550.07460.06740.0239-0.21920.0988-0.0011-0.056729.795-6.19939.655
41.6133-0.6558-0.1842.11860.44661.4979-0.0123-0.1920.17430.5612-0.130.61940.1506-0.18070.1423-0.1201-0.13310.1113-0.0533-0.14730.1037-5.3698.62635.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1OA4 - 33612 - 344
2X-RAY DIFFRACTION2PB4 - 33612 - 344
3X-RAY DIFFRACTION3QC4 - 33612 - 344
4X-RAY DIFFRACTION4RD4 - 33612 - 344

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