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- PDB-5ddi: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 5ddi
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 Angstrom resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / TRANSFERASE / Rossmann fold / NAD / GAPDH / glycolysis 1 / 10-orthophenanthroline
Function / homology
Function and homology information


Glycolysis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / Gluconeogenesis / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity ...Glycolysis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / Gluconeogenesis / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / positive regulation of type I interferon production / defense response to fungus / lipid droplet / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / NADP binding / microtubule binding / nuclear membrane / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / protein stabilization / negative regulation of translation / ribonucleoprotein complex / identical protein 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDimova, M. / Devedjiev, Y.D.
CitationJournal: To Be Published
Title: Novel enhancer binding site found in bacteria and eukaryota but not in archea.
Authors: Dimova, M. / Devedjiev, Y.D.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: 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_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,81912
Polymers107,2523
Non-polymers2,5679
Water6,900383
1
P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,42516
Polymers143,0034
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area21570 Å2
ΔGint-255 kcal/mol
Surface area49510 Å2
MethodPISA
2
S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,42516
Polymers143,0034
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area21580 Å2
ΔGint-254 kcal/mol
Surface area48960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.900, 138.970, 222.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11P
21R
12P
22S
13R
23S

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 332 / Label seq-ID: 1 - 332

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11PA
21RB
12PA
22SC
13RB
23SC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / Peptidyl-cysteine S-nitrosylase GAPDH


Mass: 35750.770 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P00355, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 383 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 54.7% w/v ammonium sulfate, 0.05 M HEPES, 0.005 M EDTA, 0.005 M 1,10-orthophenanthroline
PH range: 8

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 54851 / Num. obs: 54851 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→23.98 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.84 / SU B: 22.803 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 1699 3.1 %RANDOM
Rwork0.248 ---
obs0.2494 53174 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.17 Å2 / Biso mean: 36.604 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å20 Å2
2--0.08 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.4→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7533 0 162 383 8078
Biso mean--36.6 31.67 -
Num. residues----996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197854
X-RAY DIFFRACTIONr_bond_other_d0.0050.027467
X-RAY DIFFRACTIONr_angle_refined_deg1.721.96710668
X-RAY DIFFRACTIONr_angle_other_deg1.254317184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69624.519312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.787151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3021530
X-RAY DIFFRACTIONr_chiral_restr0.0910.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028856
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021767
X-RAY DIFFRACTIONr_mcbond_it0.4550.9833981
X-RAY DIFFRACTIONr_mcbond_other0.4550.9833980
X-RAY DIFFRACTIONr_mcangle_it0.8061.4734971
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11P170350.12
12R170350.12
21P173690.11
22S173690.11
31R170920.12
32S170920.12
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 101 -
Rwork0.322 3777 -
all-3878 -
obs--97.46 %
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)
11.0121-0.0601-0.15471.6554-0.20650.89930.09670.33770.2363-0.1196-0.2476-0.3543-0.07570.02390.15090.17-0.06670.00460.23070.15560.15525.91218.57725.029
21.5868-0.84660.12061.936-0.12490.6859-0.19360.13410.20130.7629-0.0495-0.5557-0.03220.31520.24320.5313-0.1488-0.17520.24460.07430.231418.024-8.20854.009
32.4299-0.0821-0.0011.0176-0.39380.8871-0.0872-0.5707-0.64130.040.00350.06420.1871-0.11580.08360.0597-0.01370.0520.15450.13330.184728.67953.70114.524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P1 - 502
2X-RAY DIFFRACTION2R1 - 502
3X-RAY DIFFRACTION3S1 - 502

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