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

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Basic information

Entry
Database: PDB / ID: 8hrr
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K/F100V) 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, 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
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

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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)75,9588
Polymers74,2232
Non-polymers1,7356
Water4,504250
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)151,91616
Polymers148,4464
Non-polymers3,47012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20850 Å2
ΔGint-68 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.691, 117.066, 75.727
Angle α, β, γ (deg.)90.00, 116.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 37111.523 Da / Num. of mol.: 2 / Mutation: L36S,T37K,F100V
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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Sodium formate

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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: 44734 / % possible obs: 95.7 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.984 / Rsym value: 0.08 / Χ2: 0.07 / Net I/σ(I): 15.2 / Num. measured all: 172666
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.031.80.25742051.821191.3
2.03-2.071.80.24243071.919192
2.07-2.111.80.20844022.188192.8
2.11-2.151.80.19443292.173193.5
2.15-2.21.90.18743732.413193.7
2.2-2.251.90.1644282.619194
2.25-2.311.90.14643972.972194.3
2.31-2.371.90.13644683.087195
2.37-2.441.90.12943873.513194.7
2.44-2.521.90.12244303.747195.2
2.52-2.611.90.11544554.142195.7
2.61-2.711.90.10645244.788196.2
2.71-2.8420.09544995.206196.7
2.84-2.9920.09345526.085197.2
2.99-3.1720.08345656.563198.2
3.17-3.4220.07946277.421198.9
3.42-3.762.10.07346508.326199.3
3.76-4.312.10.06546528.078199.6
4.31-5.432.10.05946407.547199.4
5.43-5020.05644837.124195.7

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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→35.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.242 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22249 2307 4.9 %RANDOM
Rwork0.17793 ---
obs0.18009 44734 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.937 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å2-0 Å2-0.9 Å2
2--2.06 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 2→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 112 250 5456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125295
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164962
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.6497207
X-RAY DIFFRACTIONr_angle_other_deg0.4831.57611410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7035669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.467532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35510851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021155
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_it2.7813.1982682
X-RAY DIFFRACTIONr_mcbond_other2.7823.1982682
X-RAY DIFFRACTIONr_mcangle_it3.7475.7343349
X-RAY DIFFRACTIONr_mcangle_other3.7485.7353350
X-RAY DIFFRACTIONr_scbond_it3.8373.7032613
X-RAY DIFFRACTIONr_scbond_other3.8373.7042614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8146.6223859
X-RAY DIFFRACTIONr_long_range_B_refined7.08334.135784
X-RAY DIFFRACTIONr_long_range_B_other7.08434.145785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.048 Å
RfactorNum. reflection% reflection
Rfree0.3 156 -
Rwork0.254 3250 -
obs--97.37 %

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