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- PDB-3pym: Structure of GAPDH 3 from S.cerevisiae at 2.0 A resolution -

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Basic information

Entry
Database: PDB / ID: 3pym
TitleStructure of GAPDH 3 from S.cerevisiae at 2.0 A resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 3
KeywordsOXIDOREDUCTASE / NAD(P)-binding Rossmann-fold domain / Alpha and beta protein / glycolysis / NAD
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / heme transport / melatonin binding / fungal-type cell wall / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / reactive oxygen species metabolic process / lipid droplet / gluconeogenesis ...Gluconeogenesis / Glycolysis / heme transport / melatonin binding / fungal-type cell wall / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / reactive oxygen species metabolic process / lipid droplet / gluconeogenesis / glycolytic process / NAD binding / NADP binding / apoptotic process / mitochondrion / RNA binding / nucleus / plasma membrane / cytoplasm / cytosol
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
MESO-ERYTHRITOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia-Saez, I. / Kozielski, F. / Job, D. / Boscheron, C.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 3
B: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1777
Polymers71,5832
Non-polymers1,5945
Water8,863492
1
A: Glyceraldehyde-3-phosphate dehydrogenase 3
B: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)146,35514
Polymers143,1664
Non-polymers3,18810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area20860 Å2
ΔGint-159 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.834, 131.052, 96.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-368-

HOH

31B-500-

HOH

41B-572-

HOH

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Components

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


Mass: 35791.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00359, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#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: Chemical ChemComp-MRY / MESO-ERYTHRITOL


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 10.5-15.5% PEG, 50mM NaAc, 1mm DTT, 1mm NAD, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 4, 2004
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→48.34 Å / Num. all: 52637 / Num. obs: 52575 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.7 % / Rmerge(I) obs: 0.094 / Rsym value: 0.091

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Processing

Software
NameVersionClassification
DNAdata collection
PHASER(CCP4 supported)phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GD1

1gd1


Resolution: 2→44.615 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 5273 10.08 %random
Rwork0.1473 ---
all0.1516 57581 --
obs0.1516 52308 99.29 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.86 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3726 Å2-0 Å20 Å2
2---1.7782 Å2-0 Å2
3----0.5944 Å2
Refinement stepCycle: LAST / Resolution: 2→44.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 105 492 5617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145222
X-RAY DIFFRACTIONf_angle_d1.5177098
X-RAY DIFFRACTIONf_dihedral_angle_d14.2271900
X-RAY DIFFRACTIONf_chiral_restr0.093833
X-RAY DIFFRACTIONf_plane_restr0.008891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06890.20284900.15094573X-RAY DIFFRACTION98
2.0689-2.15170.22045640.1464603X-RAY DIFFRACTION99
2.1517-2.24960.18575170.14264641X-RAY DIFFRACTION99
2.2496-2.36820.20664900.14874672X-RAY DIFFRACTION99
2.3682-2.51660.21415310.15434675X-RAY DIFFRACTION100
2.5166-2.71090.18895420.13874722X-RAY DIFFRACTION100
2.7109-2.98360.19785470.13934704X-RAY DIFFRACTION100
2.9836-3.41520.1914780.15494774X-RAY DIFFRACTION100
3.4152-4.30230.17755880.14784743X-RAY DIFFRACTION100
4.3023-44.62640.16365260.14754928X-RAY DIFFRACTION99
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)
11.3165-0.6438-0.27550.60930.25640.3589-0.18810.01910.20710.21210.1099-0.08680.01340.0087-0.0868-0.00060.00570.05110.039-0.03-0.017230.066126.833327.6998
20.1769-0.0897-0.09610.10640.03170.0518-0.0177-0.0456-0.03660.1065-0.01230.05410.05930.00430.03420.0869-0.03180.04560.0698-0.00570.074246.07078.907128.6861
30.1463-0.12240.00620.39480.05150.17170.01620.1172-0.0355-0.086-0.07090.00320.0796-0.03390.04170.0926-0.01580.01890.0965-0.03310.057651.25997.489512.7995
40.49480.54940.29631.04730.51140.3164-0.17430.3132-0.0509-0.21220.295-0.1011-0.07140.1668-0.10530.1063-0.06420.02020.1932-0.0280.030359.982336.6375-6.5136
50.1186-0.01080.07610.0754-0.07640.09740.01290.0840.0643-0.0846-0.0677-0.08090.01410.05680.04850.08060.01090.02160.09750.02850.116964.652947.774114.5973
60.12180.09730.09610.3024-0.00260.132-0.0333-0.00720.1369-0.07830.0030.0658-0.0157-0.04140.02920.06450.0189-0.00570.07660.01770.165851.34952.764815.5165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:115)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 116:232)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 233:293)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 2:148)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 149:218)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 219:291)

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