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- PDB-2b4r: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 2b4r
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 dehydrogenase
KeywordsOXIDOREDUCTASE / SGPP / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / GAPDH / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / Structural Genomics of Pathogenic Protozoa Consortium
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: 2.25 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
SupersessionOct 4, 2005ID: 1ZYA
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)154,20915
Polymers150,5774
Non-polymers3,63211
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21920 Å2
ΔGint-127 kcal/mol
Surface area44670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.327, 104.585, 90.838
Angle α, β, γ (deg.)90.00, 107.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
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


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


Mass: 203.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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 BL9-210.980699
SYNCHROTRONSSRL BL9-220.980699
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 4, 2005double crystal monochromator
QUANTUM 3152CCDMar 4, 2005double crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.980699 Å / Relative weight: 1
ReflectionResolution: 2.25→46.37 Å / Num. all: 54043 / Num. obs: 54043 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 49.5 Å2 / Rsym value: 0.093 / Net I/σ(I): 7.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.507 / % possible all: 87.1

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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: 1J0X

1j0x


Resolution: 2.25→46.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.801 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.392 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 2892 5.1 %RANDOM
Rwork0.18282 ---
all0.18587 54043 --
obs0.18587 54043 96.94 %-
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: 65.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.14 Å2
2---0.25 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10204 0 239 257 10700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210428
X-RAY DIFFRACTIONr_bond_other_d0.0010.029475
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9814213
X-RAY DIFFRACTIONr_angle_other_deg0.715321898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7751332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4924.293396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.111151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0431543
X-RAY DIFFRACTIONr_chiral_restr0.0590.21649
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022008
X-RAY DIFFRACTIONr_nbd_refined0.1760.22034
X-RAY DIFFRACTIONr_nbd_other0.1650.29929
X-RAY DIFFRACTIONr_nbtor_refined0.1690.25059
X-RAY DIFFRACTIONr_nbtor_other0.0790.26108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0770.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.34648503
X-RAY DIFFRACTIONr_mcbond_other0.26942740
X-RAY DIFFRACTIONr_mcangle_it1.753610616
X-RAY DIFFRACTIONr_scbond_it1.94564416
X-RAY DIFFRACTIONr_scangle_it2.817103597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.371 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.395 357 -
Rwork0.308 7082 -
obs--87.09 %
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)
11.2483-0.1511-0.23231.83410.42371.7830.27410.29330.444-0.4686-0.1903-0.401-0.29960.1536-0.0838-0.4210.00660.0307-0.23540.1252-0.154723.92414.837.297
21.2413-0.5023-0.48082.41421.01062.36450.03440.2803-0.48130.2534-0.39640.60380.742-0.4180.362-0.3913-0.07-0.0984-0.1328-0.1741-0.26664.14-17.5128.759
32.1626-1.1296-0.59311.5873-0.0510.5313-0.3495-0.39350.1420.72060.183-0.25870.28270.15580.1665-0.35640.0495-0.2455-0.4271-0.0226-0.592829.516-6.00139.312
41.1486-0.6222-0.31851.44330.28941.3334-0.0494-0.1142-0.0480.6374-0.10040.49460.1677-0.16220.1498-0.2602-0.13480.083-0.2288-0.1262-0.1104-5.7988.63935.453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1OA3 - 33611 - 344
2X-RAY DIFFRACTION2PB3 - 33611 - 344
3X-RAY DIFFRACTION3QC3 - 33611 - 344
4X-RAY DIFFRACTION4RD3 - 33611 - 344

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