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- PDB-7c5q: Crystal Structure of H177A mutant Glyceraldehyde-3-phosphate dehy... -

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Basic information

Entry
Database: PDB / ID: 7c5q
TitleCrystal Structure of H177A mutant Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli complexed with BPG at 2.13 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
Chem-DG4 / 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: 2.13 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

Downloads & links

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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)155,93229
Polymers151,2834
Non-polymers4,64825
Water17,511972
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24160 Å2
ΔGint-232 kcal/mol
Surface area43140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.674, 89.674, 341.795
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: 37820.852 Da / Num. of mol.: 4 / Mutation: H177A
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 , 7 types, 997 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.: 3 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DG4 / phosphono (2S)-2-oxidanyl-3-phosphonooxy-propanoate / glycerate 1,3-biphosphate


Mass: 266.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O10P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100mM sodium PBS pH 6.6, 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: 2.13→50 Å / Num. obs: 79577 / % possible obs: 100 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 17.75
Reflection shellResolution: 2.13→2.17 Å / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 5 / Num. unique obs: 79577 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C5F

7c5f


Resolution: 2.13→48.084 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 3931 4.96 %RANDOM
Rwork0.1379 ---
obs0.1405 79238 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→48.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10046 0 283 973 11302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110600
X-RAY DIFFRACTIONf_angle_d1.14614433
X-RAY DIFFRACTIONf_dihedral_angle_d18.4476312
X-RAY DIFFRACTIONf_chiral_restr0.0621711
X-RAY DIFFRACTIONf_plane_restr0.0071808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.15570.2591310.15362633X-RAY DIFFRACTION100
2.1557-2.1830.22741320.14352673X-RAY DIFFRACTION100
2.183-2.21170.23731410.14272591X-RAY DIFFRACTION100
2.2117-2.2420.2071580.13872670X-RAY DIFFRACTION100
2.242-2.2740.20791310.13712623X-RAY DIFFRACTION100
2.274-2.3080.18311470.1372663X-RAY DIFFRACTION100
2.308-2.34410.22311260.14072639X-RAY DIFFRACTION100
2.3441-2.38250.2061600.1362625X-RAY DIFFRACTION100
2.3825-2.42360.19811310.13312678X-RAY DIFFRACTION100
2.4236-2.46760.20281280.14012641X-RAY DIFFRACTION100
2.4676-2.51510.2231380.14242658X-RAY DIFFRACTION100
2.5151-2.56640.22081200.14782691X-RAY DIFFRACTION100
2.5664-2.62220.20671220.14152686X-RAY DIFFRACTION100
2.6222-2.68320.21981610.1392612X-RAY DIFFRACTION100
2.6832-2.75030.20061400.13912697X-RAY DIFFRACTION100
2.7503-2.82470.19371490.13512655X-RAY DIFFRACTION100
2.8247-2.90780.21771300.15442696X-RAY DIFFRACTION100
2.9078-3.00160.23011530.15262656X-RAY DIFFRACTION100
3.0016-3.10890.20771300.16372700X-RAY DIFFRACTION100
3.1089-3.23330.21711470.15832677X-RAY DIFFRACTION100
3.2333-3.38040.19641200.15052704X-RAY DIFFRACTION100
3.3804-3.55860.21851400.15072709X-RAY DIFFRACTION100
3.5586-3.78150.18941310.13712731X-RAY DIFFRACTION100
3.7815-4.07330.16451470.12222740X-RAY DIFFRACTION100
4.0733-4.4830.13271270.10382761X-RAY DIFFRACTION100
4.483-5.1310.1321530.10472751X-RAY DIFFRACTION100
5.131-6.46210.15141640.12732807X-RAY DIFFRACTION100
6.4621-48.0840.16771740.15222940X-RAY DIFFRACTION99

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