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- PDB-6m5x: A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resis... -

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Basic information

Entry
Database: PDB / ID: 6m5x
TitleA fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to inhibitor heptelidic acid
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / inhibitor / self-resistance / heptelidic acid
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 / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHypocrea virens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05990923752 Å
AuthorsYan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y.
CitationJournal: Chem Sci / Year: 2020
Title: Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance
Authors: Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y.
History
DepositionMar 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
O: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,42645
Polymers144,0874
Non-polymers5,33941
Water11,656647
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27690 Å2
ΔGint-95 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.667, 96.562, 96.699
Angle α, β, γ (deg.)90.000, 96.949, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ORPQ

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 36021.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea virens (strain Gv29-8 / FGSC 10586) (fungus)
Strain: Gv29-8 / FGSC 10586 / Gene: TRIVIDRAFT_217322 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: G9NDK9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 6 types, 688 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.059→50 Å / Num. obs: 85148 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 25.100858583 Å2 / CC1/2: 0.837 / Rmerge(I) obs: 0.126 / Net I/σ(I): 2.429
Reflection shellResolution: 2.06→2.1 Å / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.429 / Num. unique obs: 85148 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O59

4o59


Resolution: 2.05990923752→39.2901171738 Å / SU ML: 0.196588078964 / Cross valid method: FREE R-VALUE / σ(F): 1.36645748307 / Phase error: 19.557254141
RfactorNum. reflection% reflection
Rfree0.193344350312 3859 4.93270103409 %
Rwork0.150416608 --
obs0.152561571772 78233 90.4793847221 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.7337282741 Å2
Refinement stepCycle: LAST / Resolution: 2.05990923752→39.2901171738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10132 0 344 647 11123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061612022486910697
X-RAY DIFFRACTIONf_angle_d0.99939491183614479
X-RAY DIFFRACTIONf_chiral_restr0.05577738200791647
X-RAY DIFFRACTIONf_plane_restr0.005554188613731820
X-RAY DIFFRACTIONf_dihedral_angle_d15.37919942246353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.0850.255254209874960.1841796272961750X-RAY DIFFRACTION60.9844730757
2.085-2.11140.234286560402830.1878331333842001X-RAY DIFFRACTION67.4215464251
2.1114-2.13920.2425331064671000.1745206371942050X-RAY DIFFRACTION69.1540688324
2.1392-2.16850.2388038703081210.1752369883432077X-RAY DIFFRACTION72.255095332
2.1685-2.19950.2437952641661020.1706337801022209X-RAY DIFFRACTION74.9108589951
2.1995-2.23230.2415136876731110.1641495960662254X-RAY DIFFRACTION77.7193558988
2.2323-2.26720.2128274526451280.1680036644512321X-RAY DIFFRACTION79.7460110713
2.2672-2.30440.2363586592991180.165425713782454X-RAY DIFFRACTION82.9142488717
2.3044-2.34410.2076269888291210.172258929692503X-RAY DIFFRACTION85.6956237753
2.3441-2.38670.2493711267661380.1687639183582578X-RAY DIFFRACTION88.1818181818
2.3867-2.43260.2072284078891350.1801879888962635X-RAY DIFFRACTION90.3752039152
2.4326-2.48220.2248864716231370.1688047558012756X-RAY DIFFRACTION92.6056338028
2.4822-2.53620.2487013631421530.1782181995312785X-RAY DIFFRACTION96.2962962963
2.5362-2.59520.2181602075081680.1652659366052867X-RAY DIFFRACTION98.9889106327
2.5952-2.66010.2269815657321290.1672322439452945X-RAY DIFFRACTION99.2894056848
2.6601-2.7320.2211207433551400.167621745672935X-RAY DIFFRACTION99.3859082094
2.732-2.81240.2312010173151590.1674175673552879X-RAY DIFFRACTION99.1838067254
2.8124-2.90310.219148997181560.16346339612919X-RAY DIFFRACTION99.8052580331
2.9031-3.00680.1964159533211400.1681973289632943X-RAY DIFFRACTION99.5801033592
3.0068-3.12720.2247905319181470.1561034738422937X-RAY DIFFRACTION99.6767937944
3.1272-3.26940.2093252515761480.1525494203372907X-RAY DIFFRACTION99.6737357259
3.2694-3.44170.1697902654841810.1343222629162933X-RAY DIFFRACTION99.839692209
3.4417-3.65720.1922892678741690.1391754561122909X-RAY DIFFRACTION99.8378203049
3.6572-3.93930.1608840728311600.1337367351442932X-RAY DIFFRACTION99.9353587589
3.9393-4.33530.1455974573181330.1148813959492977X-RAY DIFFRACTION99.8715478484
4.3353-4.96160.1390967173031840.1140406930842915X-RAY DIFFRACTION99.8389175258
4.9616-6.2470.1786067440531480.1486441983932987X-RAY DIFFRACTION99.9043977055
6.247-39.290.1821923604261540.1551049328583016X-RAY DIFFRACTION99.3418990912

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