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- PDB-6fzh: Crystal structure of a streptococcal dehydrogenase at 1.5 Angstro... -

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Basic information

Entry
Database: PDB / ID: 6fzh
TitleCrystal structure of a streptococcal dehydrogenase at 1.5 Angstroem resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Streptococcus pyogenes / GAPDH / NAD / dehydrogenase / anacardic acid / curcumin / complement / C5a / C3a / C3
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 / Dihydrodipicolinate Reductase; domain 2 ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes MGAS8232 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGomez, S. / Querol-Garcia, J. / Sanchez-Barron, G. / Subias, M. / Gonzalez-Alsina, A. / Melchor-Tafur, C. / Franco-Hidalgo, V. / Alberti, S. / Rodriguez de Cordoba, S. / Fernandez, F.J. / Vega, M.C.
Funding support Spain, Belgium, 7items
OrganizationGrant numberCountry
Instituto de Salud Carlos IIIPI12/01667 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-66206-C2-2-R Spain
Spanish Ministry of Economy and CompetitivenessSAF2015-72961-EXP Spain
Spanish Network of Excellence on ComplementSAF2016-81876-REDT Spain
Regional Government of MadridS2010/BD-2316 Spain
Regional Government of MadridS2017/BMD-3673 Spain
European Commission, FP7 ProgrammeComplexINC (Contract No. 279039) Belgium
Citation
Journal: Front Microbiol / Year: 2019
Title: The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human ...Title: The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding.
Authors: Gomez, S. / Querol-Garcia, J. / Sanchez-Barron, G. / Subias, M. / Gonzalez-Alsina, A. / Franco-Hidalgo, V. / Alberti, S. / Rodriguez de Cordoba, S. / Fernandez, F.J. / Vega, M.C.
#1: Journal: Front Microbiol / Year: 2017
Title: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen
Authors: Querol-Garcia, J. / Fernandez, F.J. / Marin, A.V. / Gomez, S. / Fulla, D. / Melchor-Tafur, C. / Franco-Hidalgo, V. / Alberti, S. / Juanhuix, J. / Rodriguez de Cordoba, S. / Regueiro, J.R. / Vega, M.C.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6758
Polymers71,9652
Non-polymers1,7096
Water16,448913
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)147,34916
Polymers143,9314
Non-polymers3,41912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area22030 Å2
ΔGint-126 kcal/mol
Surface area44040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.266, 91.603, 106.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-336-

LYS

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Components

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


Mass: 35982.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS8232 (bacteria)
Gene: gap, gapA, plr, spyM18_0261 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: P68777, 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: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M potassium nitrate, 22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2012 / Details: FOCUSING MIRRORS IN KIRKPATRICK-BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY DIFFRACTING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→44.13 Å / Num. obs: 122574 / % possible obs: 98.53 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0598 / Rrim(I) all: 0.0707 / Net I/σ(I): 15.81
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 10880 / CC1/2: 0.527 / Rrim(I) all: 0.642 / % possible all: 88.69

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSMarch 15, 2012data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVF

3lvf


Resolution: 1.5→44.13 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 15.53
RfactorNum. reflection% reflectionSelection details
Rfree0.1628 5676 2.48 %RANDOM SELETION
Rwork0.1483 ---
obs0.1487 122305 95.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 113 913 6078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065533
X-RAY DIFFRACTIONf_angle_d1.0327560
X-RAY DIFFRACTIONf_dihedral_angle_d7.9214932
X-RAY DIFFRACTIONf_chiral_restr0.064875
X-RAY DIFFRACTIONf_plane_restr0.006988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.31921320.30495465X-RAY DIFFRACTION70
1.5171-1.53490.30981330.28415831X-RAY DIFFRACTION74
1.5349-1.55360.32791650.26196041X-RAY DIFFRACTION78
1.5536-1.57330.23441710.25216356X-RAY DIFFRACTION82
1.5733-1.5940.27831830.24936802X-RAY DIFFRACTION86
1.594-1.61580.21072120.23556903X-RAY DIFFRACTION89
1.6158-1.63890.24831680.21597280X-RAY DIFFRACTION94
1.6389-1.66340.20621920.19327778X-RAY DIFFRACTION99
1.6634-1.68940.19031910.1917749X-RAY DIFFRACTION100
1.6894-1.71710.19092030.18687747X-RAY DIFFRACTION100
1.7171-1.74670.21272050.17687774X-RAY DIFFRACTION100
1.7467-1.77840.18341950.16897780X-RAY DIFFRACTION100
1.7784-1.81260.19491920.16697806X-RAY DIFFRACTION100
1.8126-1.84960.19342010.16977734X-RAY DIFFRACTION100
1.8496-1.88990.1541820.16547827X-RAY DIFFRACTION100
1.8899-1.93380.18481870.15117740X-RAY DIFFRACTION100
1.9338-1.98220.14812130.13827776X-RAY DIFFRACTION100
1.9822-2.03580.16152090.14067801X-RAY DIFFRACTION100
2.0358-2.09570.14031830.13497744X-RAY DIFFRACTION100
2.0957-2.16330.15072190.13117746X-RAY DIFFRACTION100
2.1633-2.24060.17662070.12837780X-RAY DIFFRACTION100
2.2406-2.33040.14822280.12947742X-RAY DIFFRACTION100
2.3304-2.43640.15461750.13277742X-RAY DIFFRACTION100
2.4364-2.56480.15661590.13277820X-RAY DIFFRACTION100
2.5648-2.72550.1271930.13157810X-RAY DIFFRACTION100
2.7255-2.93590.13091840.13127792X-RAY DIFFRACTION100
2.9359-3.23130.15591770.13227745X-RAY DIFFRACTION100
3.2313-3.69870.14192080.12737775X-RAY DIFFRACTION100
3.6987-4.65910.11562020.11447752X-RAY DIFFRACTION100
4.6591-44.15370.14912070.13887769X-RAY DIFFRACTION100
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)
10.4639-0.0530.17190.6340.06090.6639-0.0147-0.06550.01230.10810.0032-0.078-0.03770.0524-0.00050.1256-0.0145-0.02670.1088-0.00640.102351.671617.4653101.6715
20.112-0.04690.05940.3327-0.00640.1267-0.0095-0.00530.03610.0496-0.0036-0.0027-0.04770.00030.01040.11520.0086-0.00290.0963-0.00170.095634.440722.683784.3762
30.6492-0.12930.01050.44850.19610.71390.01290.0666-0.0764-0.0502-0.02920.04190.0524-0.0558-0.00210.0835-0.0103-0.00680.1004-0.020.117620.5736-8.191956.3336
40.2256-0.02560.05820.165-0.00360.1172-0.00310.01360.00120.0129-0.00840.0481-0.0209-0.03470.00740.08640.01260.00430.1003-0.00760.099218.49779.918572.6178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 336 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 140 through 336 )

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