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- PDB-4lsm: Crystal structure of a glycosomal glyceraldehyde-3-phosphate dehy... -

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Basic information

Entry
Database: PDB / ID: 4lsm
TitleCrystal structure of a glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi
ComponentsGlyceraldehyde 3-phosphate dehydrogenase, cytosolic
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NAD-depenent / glucose metabolic process
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 speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi
Authors: Edwards, T.E. / Abendroth, J.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Assembly

Deposited unit
A: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic
B: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,77910
Polymers75,0802
Non-polymers1,6998
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-23 kcal/mol
Surface area25270 Å2
MethodPISA
2
A: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic
B: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic
hetero molecules

A: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic
B: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,55920
Polymers150,1604
Non-polymers3,39916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area22640 Å2
ΔGint-73 kcal/mol
Surface area42260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.490, 80.490, 203.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glyceraldehyde 3-phosphate dehydrogenase, cytosolic / / GAPDH


Mass: 37540.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053510105.230 / Plasmid: pBG1861 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4DZT1, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: TrcrA.00814.b.B1.PS01922 at 29.1 mg/mL against JCSG+ screen condition G8 (0.15 M DL-malic acid, 25% PEG3350), cryoprotectant: 15% ethylene glycol, crystal tracking ID 246268g8, unique puck ...Details: TrcrA.00814.b.B1.PS01922 at 29.1 mg/mL against JCSG+ screen condition G8 (0.15 M DL-malic acid, 25% PEG3350), cryoprotectant: 15% ethylene glycol, crystal tracking ID 246268g8, unique puck ID roi5-9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 92667 / Num. obs: 92582 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 25.482 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.4345.06736176739100
1.69-1.740.376722246608100
1.74-1.790.3057.3705786458100
1.79-1.840.2578.81676516188100
1.84-1.910.2210.45657006055100
1.91-1.970.18412.64632475877100
1.97-2.050.15914.61597915648100
2.05-2.130.14416.01569125458100
2.13-2.220.12717.75537365237100
2.22-2.330.11519.15504305011100
2.33-2.460.10620.44477734787100
2.46-2.610.09821.84446034533100
2.61-2.790.09123.21419454287100
2.79-3.010.08224.31385723963100
3.01-3.30.07825.91358403690100
3.3-3.690.07426.95327213377100
3.69-4.260.06627.77291372980100
4.26-5.220.06328.2324740253999.8
5.22-7.380.05627.8819837202499.8
7.380.05325.299132112393.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.56 Å
Translation3 Å48.56 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAD

1gad


Resolution: 1.65→48.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.175 / WRfactor Rwork: 0.136 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9259 / SU B: 2.904 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0891 / SU Rfree: 0.0734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 4627 5 %RANDOM
Rwork0.1317 ---
obs0.1337 92504 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.52 Å2 / Biso mean: 22.6967 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.14 Å20 Å2
2--0.14 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 112 645 5691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195256
X-RAY DIFFRACTIONr_bond_other_d0.0010.025085
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9787167
X-RAY DIFFRACTIONr_angle_other_deg0.778311673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27224.089203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16515866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3391532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025981
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021161
X-RAY DIFFRACTIONr_mcbond_it1.3561.2182690
X-RAY DIFFRACTIONr_mcbond_other1.3571.2172689
X-RAY DIFFRACTIONr_mcangle_it1.7661.8333371
X-RAY DIFFRACTIONr_rigid_bond_restr2.23310341
X-RAY DIFFRACTIONr_sphericity_free29.0295169
X-RAY DIFFRACTIONr_sphericity_bonded7.039510714
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 349 -
Rwork0.132 6382 -
all-6731 -
obs--100 %
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)
10.16970.0298-0.04740.32170.17910.56870.00710.03760.0077-0.05510.0002-0.0402-0.08360.0634-0.00730.1357-0.00750.01660.02210.00450.055168.381968.459514.1895
20.2690.0476-0.15380.1541-0.13410.177-0.02760.0256-0.045-0.02360.00290.02680.0401-0.02920.02470.1349-0.02950.01220.0241-0.03880.082139.626950.107232.0783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 338
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B8 - 338
4X-RAY DIFFRACTION2B401

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