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- PDB-8hrs: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 8hrs
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K/P192S) in complex with NADP
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsSTRUCTURAL PROTEIN / Dehydrogenase
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 / cytoplasm
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSon, H.F. / Kim, K.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity.
Authors: Son, H.F. / Yu, H. / Hong, J. / Lee, D. / Kim, I.K. / Kim, K.J.
History
DepositionDec 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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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
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,84811
Polymers148,5984
Non-polymers3,2507
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19800 Å2
ΔGint-78 kcal/mol
Surface area43790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.125, 99.133, 152.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 37149.527 Da / Num. of mol.: 4 / Mutation: L36S,T37K,P192S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: gap, Cgl1588, cg1791 / Production host: Escherichia coli (E. coli)
References: UniProt: Q01651, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Lithium acetate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 86317 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.987 / Rsym value: 0.082 / Χ2: 0.062 / Net I/σ(I): 7.1 / Num. measured all: 669336
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.033.30.50686381.146199.3
2.03-2.073.40.48187231.219199.5
2.07-2.113.50.43186981.252199.5
2.11-2.153.50.40487461.281199.6
2.15-2.23.50.38286621.293199.5
2.2-2.253.60.33587041.338199.6
2.25-2.313.60.29586511.369199.6
2.31-2.373.60.28286841.419199.6
2.37-2.443.70.25887071.393199.6
2.44-2.523.70.23487261.443199.6
2.52-2.613.70.21387011.434199.6
2.61-2.713.80.18687031.467199.7
2.71-2.843.90.15187111.54199.7
2.84-2.993.90.13786851.542199.7
2.99-3.174.10.10587581.577199.9
3.17-3.424.30.08787321.6241100
3.42-3.764.40.0787031.7121100
3.76-4.314.40.05487821.608199.9
4.31-5.434.40.04886961.581199.9
5.43-504.40.04887411.713199.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0403refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HRO

8hro


Resolution: 2→38.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.939 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22729 4572 5 %RANDOM
Rwork0.17059 ---
obs0.1734 86317 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.521 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-0 Å20 Å2
2--1.89 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 210 722 11096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01210556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169861
X-RAY DIFFRACTIONr_angle_refined_deg1.621.64614371
X-RAY DIFFRACTIONr_angle_other_deg0.5361.57622673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74951334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.126564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01101699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.21692
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022328
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5542.6115348
X-RAY DIFFRACTIONr_mcbond_other2.5542.6115348
X-RAY DIFFRACTIONr_mcangle_it3.654.6796678
X-RAY DIFFRACTIONr_mcangle_other3.654.686679
X-RAY DIFFRACTIONr_scbond_it3.7122.9645208
X-RAY DIFFRACTIONr_scbond_other3.7122.9655209
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6735.2617694
X-RAY DIFFRACTIONr_long_range_B_refined7.226.411658
X-RAY DIFFRACTIONr_long_range_B_other7.226.411659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å
RfactorNum. reflection% reflection
Rfree0.314 309 -
Rwork0.267 6080 -
obs--95.86 %

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