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- PDB-6nlx: Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 6nlx
TitleCrystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase from Naegleria fowleri with bound NAD
ComponentsGlyceraldehyde-3-phosphate Dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / NAD / Glyceraldehyde-3-phosphate / Dehydrogenase / GAPDH / glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
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 / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase from Naegleria fowleri with bound NAD
Authors: Higgins, T.W. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
B: Glyceraldehyde-3-phosphate Dehydrogenase
C: Glyceraldehyde-3-phosphate Dehydrogenase
D: Glyceraldehyde-3-phosphate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,48520
Polymers150,6884
Non-polymers2,79716
Water18,5731031
1
A: Glyceraldehyde-3-phosphate Dehydrogenase
B: Glyceraldehyde-3-phosphate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3188
Polymers75,3442
Non-polymers9746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-25 kcal/mol
Surface area26600 Å2
MethodPISA
2
C: Glyceraldehyde-3-phosphate Dehydrogenase
D: Glyceraldehyde-3-phosphate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,16712
Polymers75,3442
Non-polymers1,82310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-28 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 119.940, 162.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glyceraldehyde-3-phosphate Dehydrogenase


Mass: 37671.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Gene: NF0055660 / Plasmid: NafoA.00855.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A4V8H039*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 F2 (293453f2): 200mM Ammonium Acetate, 100mM Bis-Tris:HCl pH 6.5, 25% (w/v) PEG 3350: NafoA.00855.a.B1.PS38303 @ 21.4mg/mL: 15%EG: zzl0-7: aps_20170818_21idf

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→49.467 Å / Num. obs: 129448 / % possible obs: 97.4 % / Redundancy: 5.877 % / Biso Wilson estimate: 27.543 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.084 / Χ2: 1.02 / Net I/σ(I): 13.9 / Num. measured all: 760791 / Scaling rejects: 2334
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.2680.5482.8860276975096160.8350.698.6
1.85-1.96.2080.4123.8858053945993510.9070.45198.9
1.9-1.956.1580.354.7456182922991230.9240.38498.9
1.95-2.016.070.2786.0753791897688620.9410.30698.7
2.01-2.085.9780.2267.4251337871285870.9620.24998.6
2.08-2.155.8750.198.7448743845482970.9730.2198.1
2.15-2.235.7510.15410.6145805810179650.980.17198.3
2.23-2.325.6940.13312.0143393780476210.9850.14897.7
2.32-2.435.6540.11613.5841706755673770.9870.12897.6
2.43-2.555.6330.10315.0539375719369900.9890.11497.2
2.55-2.685.6070.08917.137076685366130.9910.09996.5
2.68-2.855.6040.07819.0135138650662700.9930.08796.4
2.85-3.045.6270.06721.4732976613658600.9940.07495.5
3.04-3.295.6980.05824.4830827570454100.9950.06494.8
3.29-3.65.7370.05226.8628660527549960.9960.05794.7
3.6-4.025.7680.04728.5126500480545940.9970.05195.6
4.02-4.655.8540.0430.2524084424641140.9980.04496.9
4.65-5.696.0120.03730.7321258363535360.9990.0497.3
5.69-8.056.0580.03530.3716708286627580.9990.03896.2
8.05-49.4675.9040.02631.98903165415080.9990.02991.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8F

1u8f


Resolution: 1.8→49.467 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.66
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 2019 1.56 %0
Rwork0.1685 ---
obs0.1691 129402 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.9 Å2 / Biso mean: 29.4725 Å2 / Biso min: 7.63 Å2
Refinement stepCycle: final / Resolution: 1.8→49.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10175 0 192 1037 11404
Biso mean--31.07 34.86 -
Num. residues----1337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.8450.30981500.23649113926399
1.845-1.89480.28291380.23399122926099
1.8948-1.95060.25231440.22169156930099
1.9506-2.01360.26131390.20789140927999
2.0136-2.08550.23021540.19929112926698
2.0855-2.1690.20441650.19029094925998
2.169-2.26770.20431220.18489131925398
2.2677-2.38730.24121440.18369046919097
2.3873-2.53690.21781430.18299073921697
2.5369-2.73270.22741340.17799026916097
2.7327-3.00770.21391490.17448971912096
3.0077-3.44280.21321300.15918928905895
3.4428-4.33720.15081310.13279099923096
4.3372-49.48540.161760.13149372954896
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)
11.8798-0.9099-0.42221.38020.5773.3144-0.094-0.26060.43770.0459-0.07410.1917-0.6374-0.40040.10150.31150.1252-0.06820.3365-0.13240.34386.217714.292328.4066
20.63010.1128-0.04510.43610.47191.7320.0032-0.22860.1040.1407-0.09920.0862-0.0436-0.1790.03750.17850.02420.01140.2442-0.06380.145123.91862.270942.5536
31.6137-0.63840.04410.7224-0.1941.1884-0.00970.0708-0.0572-0.15330.0694-0.3192-0.02510.1794-0.02880.0961-0.02150.03580.181-0.06820.244159.0033-12.036412.0826
42.2621-0.6118-0.48381.9330.370.9767-0.0695-0.1293-0.34040.29790.1611-0.25550.30260.3104-0.06680.13130.0637-0.04150.2758-0.00310.280161.214-19.810929.1002
52.12480.69661.43590.57740.63422.4560.0038-0.1898-0.07760.13970.087-0.15370.07570.2631-0.09270.13120.0455-0.02990.2177-0.02650.143843.1583-8.516635.6331
62.30640.93961.67180.55470.78551.48010.1852-0.1665-0.4820.23960.0052-0.15260.30820.2811-0.20150.20560.0628-0.03610.32250.01510.170543.2456-10.988138.4498
70.590.56660.69231.17350.30131.43370.0885-0.3440.00150.31050.0174-0.10740.1490.1798-0.11810.17360.0474-0.02760.3233-0.05250.135743.2699-2.242741.1212
80.0570.07750.18220.57830.19661.4662-0.0903-0.3740.41760.11590.0505-0.2869-0.2860.35590.00370.2231-0.0531-0.04910.3836-0.14050.257254.62227.853238.3913
90.44060.47010.07860.5169-0.0711.27160.03-0.24890.04940.11880.0754-0.1953-0.12350.1124-0.09140.1316-0.0099-0.0370.2796-0.07630.172753.4251-0.795134.9702
101.05560.34410.46991.93260.81872.15970.145-0.1623-0.29990.231-0.05670.05390.3864-0.1642-0.06940.1616-0.0411-0.02090.13150.02920.199819.8521-27.488416.7986
110.68090.22970.30310.52890.22410.8945-0.03190.1256-0.0414-0.12440.00850.0507-0.1106-0.07140.0240.11430.0143-0.01330.1222-0.0190.104519.9367-8.8822-0.5352
120.21960.3855-0.02751.7504-0.54161.2695-0.2986-0.12520.397-0.0139-0.0683-0.0179-1.14710.20050.21690.8252-0.159-0.21890.1944-0.05270.483445.643328.662916.6476
131.15320.32560.51780.7695-0.06041.4577-0.17230.26040.325-0.22060.0707-0.04-0.52480.16830.00760.3586-0.0816-0.03330.15890.0560.208937.433313.1956-2.0051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 112 )A-3 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 333 )A113 - 333
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 84 )B1 - 84
4X-RAY DIFFRACTION4chain 'B' and (resid 85 through 148 )B85 - 148
5X-RAY DIFFRACTION5chain 'B' and (resid 149 through 196 )B149 - 196
6X-RAY DIFFRACTION6chain 'B' and (resid 197 through 224 )B197 - 224
7X-RAY DIFFRACTION7chain 'B' and (resid 225 through 251 )B225 - 251
8X-RAY DIFFRACTION8chain 'B' and (resid 252 through 284 )B252 - 284
9X-RAY DIFFRACTION9chain 'B' and (resid 285 through 333 )B285 - 333
10X-RAY DIFFRACTION10chain 'C' and (resid -1 through 110 )C-1 - 110
11X-RAY DIFFRACTION11chain 'C' and (resid 111 through 333 )C111 - 333
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 112 )D1 - 112
13X-RAY DIFFRACTION13chain 'D' and (resid 113 through 332 )D113 - 333

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