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- PDB-7c5p: Crystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from ... -

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Basic information

Entry
Database: PDB / ID: 7c5p
TitleCrystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with G3P at 2.35 Angstrom resolution.
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / EcGAPDH 1 / NAD
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / identical protein binding
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
GLYCERALDEHYDE-3-PHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhang, L. / Liu, M.R. / Bao, L.Y. / Yao, Y.C. / Bostrom, I.K. / Wang, Y.D. / Chen, A.Q. / Li, J.X. / Gu, S.H. / Ji, C.N.
Funding support China, 2items
OrganizationGrant numberCountry
National Key Research and Development Program of China2016YFA0500600 China
Science and Technology Research Program of Shanghai19DZ2282100 China
CitationJournal: Biomolecules / Year: 2021
Title: Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid.
Authors: Zhang, L. / Liu, M. / Bao, L. / Bostrom, K.I. / Yao, Y. / Li, J. / Gu, S. / Ji, C.
History
DepositionMay 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)155,53822
Polymers151,5524
Non-polymers3,98618
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23770 Å2
ΔGint-235 kcal/mol
Surface area43230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.339, 90.339, 341.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 4 molecules OPQR

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 37887.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ECBD_2224 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A140NCK4, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 633 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 100mM sodium PBS pH 6.1, 16%(w/v) PEG 1000, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.35→50.01 Å / Num. obs: 60156 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 14
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 5632 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C5F

7c5f


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.655 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20975 3003 5 %RANDOM
Rwork0.15497 ---
obs0.15778 56884 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.346 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å2-0 Å2
2--1.08 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10083 0 246 615 10944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910596
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210143
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.98514427
X-RAY DIFFRACTIONr_angle_other_deg1.012323412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22751352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16925.296406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.678151787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0051536
X-RAY DIFFRACTIONr_chiral_restr0.0940.21710
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211860
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022234
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_it2.2453.0885390
X-RAY DIFFRACTIONr_mcbond_other2.2383.0885389
X-RAY DIFFRACTIONr_mcangle_it3.3414.6216748
X-RAY DIFFRACTIONr_mcangle_other3.3434.6216749
X-RAY DIFFRACTIONr_scbond_it3.0463.355206
X-RAY DIFFRACTIONr_scbond_other3.0413.3485202
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4744.8797674
X-RAY DIFFRACTIONr_long_range_B_refined6.03424.44612015
X-RAY DIFFRACTIONr_long_range_B_other6.03324.43211994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 194 -
Rwork0.191 3855 -
obs--93.08 %

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