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

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Basic information

Entry
Database: PDB / ID: 8hro
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 in complex with NAD
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 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 / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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

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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)75,6424
Polymers74,3152
Non-polymers1,3272
Water70339
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)151,2848
Polymers148,6304
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area18690 Å2
ΔGint-109 kcal/mol
Surface area44270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.730, 117.348, 75.815
Angle α, β, γ (deg.)90.00, 116.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 37157.570 Da / Num. of mol.: 2
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8K, HEPES

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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: 2.59→50 Å / Num. obs: 20397 / % possible obs: 92.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.111 / Χ2: 0.09 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.59-2.641.80.27417680.954184.5
2.64-2.6920.2618351.129185.3
2.69-2.7420.22718701.31185.2
2.74-2.82.10.20519091.419189.6
2.8-2.862.10.19819121.403188.7
2.86-2.932.20.1918891.709188.8
2.93-32.20.1719511.894190.2
3-3.082.40.15919472.068191.5
3.08-3.172.40.1319652.211191.5
3.17-3.282.50.12319792.684193.4
3.28-3.392.60.12320503.436194.6
3.39-3.532.60.10720203.765193.7
3.53-3.692.80.1119955.535193.2
3.69-3.882.80.11520326.407194.8
3.88-4.1330.10221107.344196.3
4.13-4.453.10.120808.882198.8
4.45-4.893.20.08621068.071198.6
4.89-5.63.20.08221487.333199
5.6-7.053.40.07921357.085199.8
7.05-503.60.069213711.473199.3

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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: 1DBV

1dbv


Resolution: 2.59→44.81 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.147 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27154 992 4.6 %RANDOM
Rwork0.18657 ---
obs0.19025 20397 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.959 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å2-0 Å2-2.5 Å2
2---0.38 Å20 Å2
3---4 Å2
Refinement stepCycle: 1 / Resolution: 2.59→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 0 88 39 5210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125265
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164926
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6457174
X-RAY DIFFRACTIONr_angle_other_deg0.4581.57411327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.955667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.148532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20410844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021157
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_it3.8374.5322674
X-RAY DIFFRACTIONr_mcbond_other3.834.5332674
X-RAY DIFFRACTIONr_mcangle_it5.8398.1363339
X-RAY DIFFRACTIONr_mcangle_other5.8398.1373340
X-RAY DIFFRACTIONr_scbond_it5.0925.1772591
X-RAY DIFFRACTIONr_scbond_other5.0915.1782592
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1799.2413836
X-RAY DIFFRACTIONr_long_range_B_refined10.6552.135731
X-RAY DIFFRACTIONr_long_range_B_other10.64952.135732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.594→2.661 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 71 -
Rwork0.285 1349 -
obs--86.8 %

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