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- PDB-9y4u: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GA... -

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Basic information

Entry
Database: PDB / ID: 9y4u
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / GAPDH
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 / cytoplasm
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae NCCP11945 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)
Authors: Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionSep 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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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)74,9864
Polymers73,6602
Non-polymers1,3272
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-32 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.189, 123.985, 130.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 36829.789 Da / Num. of mol.: 2 / Fragment: residues 24-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae NCCP11945 (bacteria)
Gene: NGK_2321 / Plasmid: NegoA.00617.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4RPP8, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Berkeley D4: 25% (w/v) PEG 3350, 100 mM sodium acetate pH 4.5. 2mM NAD addied prior to crystallization, plate 20205 well D4 drop 3 , Puck: PSL2003, Cryo: 80% crystallant + 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 9, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→48.19 Å / Num. obs: 56062 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Χ2: 0.99 / Net I/σ(I): 18.9 / Num. measured all: 744592
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 1.743 / Num. measured all: 47577 / Num. unique obs: 3590 / CC1/2: 0.748 / Rpim(I) all: 0.495 / Rrim(I) all: 1.813 / Χ2: 0.99 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(2.0_5778: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.19 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 2808 5.01 %
Rwork0.175 --
obs0.1769 56044 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 88 267 5054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014905
X-RAY DIFFRACTIONf_angle_d1.1316688
X-RAY DIFFRACTIONf_dihedral_angle_d17.8381853
X-RAY DIFFRACTIONf_chiral_restr0.065799
X-RAY DIFFRACTIONf_plane_restr0.013853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.42471330.44812659X-RAY DIFFRACTION100
1.93-1.970.40991200.36772637X-RAY DIFFRACTION100
1.97-2.010.37571370.31892624X-RAY DIFFRACTION100
2.01-2.050.29931430.25852620X-RAY DIFFRACTION100
2.05-2.090.2621470.21922635X-RAY DIFFRACTION100
2.09-2.140.24921630.19422622X-RAY DIFFRACTION100
2.14-2.190.22941420.17482633X-RAY DIFFRACTION100
2.19-2.250.21161580.17212603X-RAY DIFFRACTION100
2.25-2.320.24861330.18252655X-RAY DIFFRACTION100
2.32-2.390.25951280.19282647X-RAY DIFFRACTION100
2.39-2.480.26241220.20712670X-RAY DIFFRACTION100
2.48-2.580.25211520.20282650X-RAY DIFFRACTION100
2.58-2.70.21391530.18552640X-RAY DIFFRACTION100
2.7-2.840.20521540.17212644X-RAY DIFFRACTION100
2.84-3.020.23761510.18252647X-RAY DIFFRACTION100
3.02-3.250.24021340.18912684X-RAY DIFFRACTION100
3.25-3.580.21011280.1672700X-RAY DIFFRACTION100
3.58-4.090.18171540.1552663X-RAY DIFFRACTION100
4.09-5.150.15511180.12072758X-RAY DIFFRACTION100
5.16-48.190.19051380.16942845X-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)
13.1198-0.4476-1.06234.64220.65234.0548-0.1516-0.2644-0.2530.86030.1685-0.2170.61850.10780.03420.44780.0371-0.08130.2637-0.00830.393731.8708-8.123142.6689
20.5847-0.6439-0.47653.6231.00381.54070.01650.0583-0.00470.1149-0.04020.01540.1255-0.01550.0460.2453-0.0057-0.05470.30550.01460.283918.542511.398340.052
30.7719-0.01280.51234.00631.08712.3688-0.0016-0.05680.09190.3511-0.13760.35150.0589-0.31120.1370.2697-0.03390.01550.3568-0.0140.330713.588813.957347.6242
44.5418-0.3978-1.77613.03790.59073.5437-0.0747-0.3143-0.13690.26410.0724-0.1067-0.03660.26490.01050.36890.02870.01330.32640.02340.271635.956541.193581.3388
51.04920.12881.00381.48370.79253.9545-0.0378-0.15910.05850.0096-0.09540.2535-0.3039-0.39670.14590.31260.08110.03220.3554-0.01160.338519.212945.464971.8748
61.40141.2987-0.90074.2121-0.24733.31840.1798-0.1767-0.19520.3039-0.21570.03340.2985-0.1219-0.04920.2821-0.0057-0.03840.3144-0.03390.272919.144226.940858.4503
70.84180.3310.39381.86731.02872.3930.01640.0287-0.0143-0.0482-0.06160.1156-0.1224-0.13610.04270.3230.05880.00340.31060.0080.290923.47936.926154.4034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 333 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 84 )
5X-RAY DIFFRACTION5chain 'B' and (resid 85 through 166 )
6X-RAY DIFFRACTION6chain 'B' and (resid 167 through 206 )
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 334 )

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