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- PDB-6io6: Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A at non-ca... -

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Basic information

Entry
Database: PDB / ID: 6io6
TitleSilver-bound Glyceraldehyde-3-phosphate dehydrogenase A at non-catalytic site
ComponentsGlyceraldehyde-3-phosphate dehydrogenase A
KeywordsCYTOSOLIC PROTEIN / silver / 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 / identical protein binding / membrane / cytosol
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 / Dihydrodipicolinate Reductase; domain 2 ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SILVER ION / Glyceraldehyde-3-phosphate dehydrogenase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWang, H. / Sun, H. / Wang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17305415P Hong Kong
CitationJournal: Chem Sci / Year: 2019
Title: Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis ofE. coli.
Authors: Wang, H. / Wang, M. / Yang, X. / Xu, X. / Hao, Q. / Yan, A. / Hu, M. / Lobinski, R. / Li, H. / Sun, H.
History
DepositionOct 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5033
Polymers35,2871
Non-polymers2162
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-5 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.260, 122.260, 157.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 35287.102 Da / Num. of mol.: 1 / Mutation: D79G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: gapA, b1779, JW1768 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 4.18 Å3/Da / Density % sol: 70.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Malic acid, PEG3350 20% / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2018
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→48.32 Å / Num. obs: 17924 / % possible obs: 99.9 % / Redundancy: 26.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.051 / Rrim(I) all: 0.256 / Net I/σ(I): 8.8 / Num. measured all: 480506 / Scaling rejects: 2808
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.64-2.7127.13.3543562813150.70.6893.432299.4
11.81-48.3221.30.14151742430.9780.0310.14414.898.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260:000)refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASER2.7.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAD

1gad


Resolution: 2.64→48.321 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 867 4.85 %
Rwork0.2024 17022 -
obs0.2042 17889 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.15 Å2 / Biso mean: 83.4904 Å2 / Biso min: 39.42 Å2
Refinement stepCycle: final / Resolution: 2.64→48.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 2 2 2415
Biso mean--93.55 88.46 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6401-2.80550.37261550.337127582913
2.8055-3.02210.2631560.258827992955
3.0221-3.32620.28841550.226927862941
3.3262-3.80730.28021210.229528262947
3.8073-4.79620.21091310.177228672998
4.7962-48.3290.21981490.180329863135
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38651.84341.22862.80890.07323.4733-0.1653-0.13150.4067-0.2122-0.1720.5216-0.1805-0.20110.40120.42440.07070.02420.4678-0.06820.513640.7913113.197535.1328
24.85043.6250.62264.40870.91762.61980.0250.5956-0.6001-0.62810.1572-0.31690.54630.6357-0.06570.78670.01040.01670.4792-0.11920.456347.2525101.635120.0886
32.6081.2869-0.2023.2256-1.36413.7733-0.26290.23130.1495-0.3728-0.0233-0.09040.0345-0.04970.35840.56550.0423-0.05960.4792-0.07840.530445.3145111.236324.1905
43.09833.312-0.4273.5732-0.80392.5166-0.00150.05540.9268-0.20590.05861.2216-0.3542-0.412-0.12080.8020.1591-0.24720.59610.00291.058739.9082132.732918.5575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 150 through 252 )A150 - 252
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 280 )A253 - 280
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 331 )A281 - 331
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 149 )A3 - 149

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