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- PDB-3cps: Crystal structure of Cryptosporidium parvum glyceraldehyde-3-phos... -

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Basic information

Entry
Database: PDB / ID: 3cps
TitleCrystal structure of Cryptosporidium parvum glyceraldehyde-3-phosphate dehydrogenase
ComponentsGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / glycolysis / malaria / structural genomics / Structural Genomics Consortium / SGC
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. ...Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Pizarro, J. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Cryptosporidium parvum glyceraldehyde-3-phosphate dehydrogenase.
Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Pizarro, J. / Hills, T.
History
DepositionApr 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: Glyceraldehyde 3-phosphate dehydrogenase
B: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4464
Polymers76,1192
Non-polymers1,3272
Water6,612367
1
A: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7232
Polymers38,0591
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7232
Polymers38,0591
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules

B: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules

B: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,8928
Polymers152,2384
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area14720 Å2
ΔGint-94.3 kcal/mol
Surface area44120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.830, 135.220, 67.923
Angle α, β, γ (deg.)90.000, 103.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21B-533-

HOH

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Components

#1: Protein Glyceraldehyde 3-phosphate dehydrogenase


Mass: 38059.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Species: Cryptosporidium parvum / Strain: Iowa type II / Gene: cgd6_3790 / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q5CWT6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M Tri-lithium citrate, 25% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 55840 / Num. obs: 55840 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 27.22 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.097 / Χ2: 1.072 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.4 / Num. unique all: 5528 / Rsym value: 0.638 / Χ2: 0.717 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.09 Å
Translation2.5 Å33.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B4R

2b4r


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.673 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.193 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2817 5.1 %RANDOM
Rwork0.239 ---
all0.242 55480 --
obs0.242 55480 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.613 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å21.33 Å2
2---1.58 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4959 0 88 367 5414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225148
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9887003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0925.263190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08515838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.171518
X-RAY DIFFRACTIONr_chiral_restr0.1120.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023792
X-RAY DIFFRACTIONr_nbd_refined0.1960.22474
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.239
X-RAY DIFFRACTIONr_mcbond_it0.4731.53383
X-RAY DIFFRACTIONr_mcangle_it0.68525323
X-RAY DIFFRACTIONr_scbond_it1.28232011
X-RAY DIFFRACTIONr_scangle_it1.7764.51680
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 188 -
Rwork0.309 3854 -
all-4042 -
obs-5528 99.14 %
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)
12.722-1.6408-1.76342.50720.32871.4976-0.1549-0.3373-0.12270.41190.15490.14940.10650.072100.04190.0151-0.0003-0.01330.0276-0.070223.68789.17920.287
21.5310.8173-0.66032.4087-0.42950.8431-0.0253-0.0740.03720.14950.04450.34560.0696-0.0947-0.01920.01860.03880.0016-0.01740.0032-0.062718.592104.30518.234
30.0075-0.02730.03393.1781.86531.4373-0.0161-0.01110.0249-0.135-0.11880.4251-0.1454-0.20260.1349-0.06590.0137-0.0485-0.01040.0023-0.048128.845104.6770.531
41.18690.2173-0.33651.6973-0.11690.64010.0235-0.1290.11680.28480.0434-0.0239-0.1540.0488-0.06690.01220.0219-0.0289-0.0449-0.0106-0.105939.062109.38514.846
53.0767-1.50391.71492.6243-0.21971.1583-0.258-0.26770.09840.36760.1268-0.2148-0.0875-0.03550.13110.03720.0402-0.08310.0094-0.0469-0.067516.509155.44420.41
61.36920.13760.05953.63360.15781.7232-0.0805-0.10590.10950.11230.0565-0.5298-0.12450.19360.024-0.02260.0412-0.0860.0189-0.00660.002925.615143.68119.637
70.259-0.3870.01881.3042-0.37460.6353-0.0424-0.0694-0.08350.07930.0242-0.0080.09750.03040.0182-0.02270.0061-0.0263-0.0412-0.0018-0.09023.671135.4978.996
81.87740.45560.93730.85340.66831.62940.1178-0.1915-0.09160.10930.0272-0.11480.0882-0.0226-0.145-0.04030.0153-0.0092-0.05580.0172-0.10017.719136.08616.762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 7318 - 73
2X-RAY DIFFRACTION2AA74 - 18974 - 189
3X-RAY DIFFRACTION3AA190 - 248190 - 248
4X-RAY DIFFRACTION4AA249 - 354249 - 354
5X-RAY DIFFRACTION5BB18 - 7318 - 73
6X-RAY DIFFRACTION6BB74 - 16774 - 167
7X-RAY DIFFRACTION7BB168 - 319168 - 319
8X-RAY DIFFRACTION8BB320 - 354320 - 354

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