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- PDB-6fzi: Crystal Structure of a Clostridial Dehydrogenase at 2.55 Angstroe... -

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Basic information

Entry
Database: PDB / ID: 6fzi
TitleCrystal Structure of a Clostridial Dehydrogenase at 2.55 Angstroems Resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Clostridium perfringens / GAPDH / NAD / dehydrogenase / anacardic acid / curcumin / complement / C5a / C3a / C3
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding
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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens SM101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.1Jan 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
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,01130
Polymers141,6014
Non-polymers4,41026
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25470 Å2
ΔGint-119 kcal/mol
Surface area41580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.280, 101.610, 92.820
Angle α, β, γ (deg.)90.00, 107.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 35400.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens SM101 (bacteria)
Gene: gap, CPR_1301 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta pLysS
References: UniProt: Q0STD4, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 87 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M sodium acetate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2014 / Details: KIRKPATRICK-BAEZ FOCUSING SYSTEM
RadiationMonochromator: CHANNEL-CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→57.67 Å / Num. obs: 42341 / % possible obs: 99.61 % / Redundancy: 4.2 % / Biso Wilson estimate: 67.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07224 / Rpim(I) all: 0.0391 / Rrim(I) all: 0.08253 / Net I/σ(I): 12.66
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.9875 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 4184 / CC1/2: 0.605 / Rpim(I) all: 0.5292 / Rrim(I) all: 1.126 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSJanuary 10, 2014data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FZH

6fzh


Resolution: 2.55→54.783 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 25.62
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4093 4.99 %RANDOM SELECTION
Rwork0.1636 ---
obs0.1662 42320 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.65 Å2
Refinement stepCycle: LAST / Resolution: 2.55→54.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9914 0 292 61 10267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910365
X-RAY DIFFRACTIONf_angle_d1.16714060
X-RAY DIFFRACTIONf_dihedral_angle_d16.7236211
X-RAY DIFFRACTIONf_chiral_restr0.0651657
X-RAY DIFFRACTIONf_plane_restr0.0071803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.580.42121390.33192588X-RAY DIFFRACTION97
2.58-2.61150.37761410.31442730X-RAY DIFFRACTION98
2.6115-2.64450.35351420.29112680X-RAY DIFFRACTION99
2.6445-2.67930.31851430.27942691X-RAY DIFFRACTION98
2.6793-2.7160.33351420.2652704X-RAY DIFFRACTION99
2.716-2.75480.33681390.25962637X-RAY DIFFRACTION98
2.7548-2.79590.31591430.26052758X-RAY DIFFRACTION99
2.7959-2.83960.33581370.26592623X-RAY DIFFRACTION98
2.8396-2.88620.30521410.26432667X-RAY DIFFRACTION99
2.8862-2.93590.29271400.23432734X-RAY DIFFRACTION98
2.9359-2.98930.26681400.22762712X-RAY DIFFRACTION99
2.9893-3.04680.32671440.22772693X-RAY DIFFRACTION99
3.0468-3.1090.27391450.2092682X-RAY DIFFRACTION99
3.109-3.17660.25841430.20682727X-RAY DIFFRACTION99
3.1766-3.25050.27731380.19852614X-RAY DIFFRACTION97
3.2505-3.33180.23991430.19082694X-RAY DIFFRACTION97
3.3318-3.42180.22681350.17552672X-RAY DIFFRACTION98
3.4218-3.52250.19581440.17022702X-RAY DIFFRACTION98
3.5225-3.63620.23731450.16172672X-RAY DIFFRACTION98
3.6362-3.76610.22421420.1582649X-RAY DIFFRACTION98
3.7661-3.91690.20931450.14472766X-RAY DIFFRACTION99
3.9169-4.09510.19071420.13362674X-RAY DIFFRACTION99
4.0951-4.31090.18311450.12872733X-RAY DIFFRACTION98
4.3109-4.58090.17161400.11332678X-RAY DIFFRACTION98
4.5809-4.93430.15871380.12212683X-RAY DIFFRACTION99
4.9343-5.43050.17651400.11862711X-RAY DIFFRACTION99
5.4305-6.21540.21651400.13972709X-RAY DIFFRACTION98
6.2154-7.82710.16761380.15462679X-RAY DIFFRACTION98
7.8271-54.79590.16181390.13462674X-RAY DIFFRACTION98
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)
12.89320.01970.4322.73510.5046.09680.04970.1596-0.2234-0.1221-0.01150.790.6401-0.9711-0.04880.5206-0.0833-0.07630.55560.06030.7141-16.7789-13.559316.6243
21.8972-0.0583-0.25891.6641-0.22442.20830.04980.53820.2228-0.6250.05440.4075-0.0807-0.4081-0.10350.53470.0202-0.10570.53450.0630.477-3.11381.77851.2385
33.2320.2802-1.17877.5008-1.70035.3277-0.15850.2477-0.568-0.43910.0305-0.62981.16040.71470.13960.62290.15060.00120.5659-0.08330.47822.6453-25.357122.0302
41.96760.17820.8431.9389-0.19293.33680.135-0.2581-0.11380.354-0.0578-0.18090.26020.4266-0.06640.39420.01620.00410.4774-0.00090.381417.684-9.535242.2195
55.77862.3486-0.10295.8667-1.89386.9655-0.0089-0.11880.3714-0.3086-0.187-0.7825-0.44441.70980.2040.5121-0.10120.04790.80950.01860.526234.1112.12123.093
62.23750.01470.19542.396-0.12326.0453-0.19310.01130.97740.6295-0.3399-0.3782-2.29891.48480.48341.0886-0.3294-0.06690.90740.09180.814335.872523.725317.5219
75.81314.6739-1.23338.0912-1.25532.5509-0.37960.0935-0.19-0.6524-0.3592-1.4361-0.62681.24150.66270.6724-0.110.01531.01880.23550.667235.925316.57580.4311
82.2609-0.0706-1.42051.337-0.48234.33060.07120.38480.199-0.454-0.0367-0.0557-0.44890.176-0.07220.5428-0.03530.0120.52790.09290.517516.37669.2551.7024
92.05980.18510.52883.03970.32783.4124-0.07810.46270.0847-0.3943-0.0298-0.33620.09120.68370.09530.45390.02670.09390.60010.05220.418924.35351.75112.271
101.9275-0.06610.15444.56830.61246.81350.23640.07550.70850.10140.07440.951-0.8953-0.8171-0.2090.61430.12020.10610.46610.10370.8384-7.201423.926225.3682
111.72720.2140.53782.6473-0.23995.93960.0343-0.06870.76390.24110.09750.4053-1.5804-0.2133-0.15110.81850.07690.19330.5092-0.02930.8915-3.607330.91636.5383
122.685-0.1679-1.121.18060.37683.59530.1078-0.32130.37830.3449-0.04340.2676-0.3833-0.0216-0.08460.46940.0030.06040.3597-0.04510.49582.25416.601543.4043
133.2656-0.1856-0.27752.3011-0.19954.34540.0131-0.16360.34840.1534-0.0923-0.0601-0.2612-0.24860.05960.4292-0.02540.14670.3783-0.010.5004-3.7518.412745.3078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 331 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 118 )
4X-RAY DIFFRACTION4chain 'B' and (resid 119 through 332 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 56 )
6X-RAY DIFFRACTION6chain 'C' and (resid 57 through 128 )
7X-RAY DIFFRACTION7chain 'C' and (resid 129 through 149 )
8X-RAY DIFFRACTION8chain 'C' and (resid 150 through 264 )
9X-RAY DIFFRACTION9chain 'C' and (resid 265 through 332 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 56 )
11X-RAY DIFFRACTION11chain 'D' and (resid 57 through 149 )
12X-RAY DIFFRACTION12chain 'D' and (resid 150 through 294 )
13X-RAY DIFFRACTION13chain 'D' and (resid 295 through 332 )

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