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- PDB-8fuy: Glucose-6-phosphate 1-dehydrogenase (G6PDH) from Crithidia fascic... -

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Basic information

Entry
Database: PDB / ID: 8fuy
TitleGlucose-6-phosphate 1-dehydrogenase (G6PDH) from Crithidia fasciculata (citrate bound)
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyCITRIC ACID
Function and homology information
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle 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 DirectorOD030394 United States
CitationJournal: To be published
Title: Glucose-6-phosphate 1-dehydrogenase (G6PDH) from Crithidia fasciculata (citrate bound)
Authors: Liu, L. / Battaile, K.P. / Lovell, S.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0428
Polymers129,2022
Non-polymers8396
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-38 kcal/mol
Surface area38420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.510, 124.906, 161.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glucose-6-phosphate 1-dehydrogenase


Mass: 64601.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Plasmid: CrfaA.01031.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG3350, 0.2M diammonium citrate, 0.1M citrate. Tray: Liu-S-062 well C9, Puck: PSL1007, Cryo: 20% PEG 200 + 80% crystallant

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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: Dec 10, 2022
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: 2.45→161.99 Å / Num. obs: 45597 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 15.8 / Num. measured all: 528095
Reflection shellResolution: 2.45→2.51 Å / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 1.528 / Num. measured all: 40453 / Num. unique obs: 3324 / CC1/2: 0.832 / Rpim(I) all: 0.454 / Rrim(I) all: 1.595 / Χ2: 1.02 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.55 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 2182 4.8 %
Rwork0.2028 --
obs0.204 45475 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7583 0 54 10 7647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047793
X-RAY DIFFRACTIONf_angle_d0.75710550
X-RAY DIFFRACTIONf_dihedral_angle_d14.3112886
X-RAY DIFFRACTIONf_chiral_restr0.0521157
X-RAY DIFFRACTIONf_plane_restr0.0051378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.50.29151290.27122683X-RAY DIFFRACTION100
2.5-2.560.33291330.28432698X-RAY DIFFRACTION100
2.56-2.630.34431230.29112679X-RAY DIFFRACTION100
2.63-2.70.28411060.27722699X-RAY DIFFRACTION100
2.7-2.780.33731110.25432687X-RAY DIFFRACTION100
2.78-2.870.25181490.24132684X-RAY DIFFRACTION100
2.87-2.970.27231300.25192695X-RAY DIFFRACTION100
2.97-3.090.28211460.24842664X-RAY DIFFRACTION100
3.09-3.230.30971540.26332716X-RAY DIFFRACTION100
3.23-3.40.28191380.23722666X-RAY DIFFRACTION100
3.4-3.610.231430.212708X-RAY DIFFRACTION100
3.61-3.890.22991460.20162685X-RAY DIFFRACTION100
3.89-4.280.20181270.17572736X-RAY DIFFRACTION100
4.28-4.90.17851560.15472715X-RAY DIFFRACTION100
4.9-6.170.23321290.19222777X-RAY DIFFRACTION100
6.17-43.550.1731620.16992801X-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)
12.89410.8895-0.08213.79750.51255.12160.3657-0.74250.00190.8373-0.41810.11730.749-0.49790.07071.004-0.18150.02340.94390.03490.499-2.102944.080312.6124
21.60480.6107-0.43731.002-0.31532.5956-0.1531-0.3453-0.33910.0349-0.1469-0.08360.66210.08980.20060.70410.07280.10420.41670.11450.50422.52933.4185-17.5646
34.3790.3604-1.79215.22810.05446.0316-0.2228-0.7225-0.7156-0.1208-0.8897-1.07281.00861.38450.77640.5910.27990.26251.05390.35031.095447.249349.5318-48.9186
41.1028-0.44431.73161.4825-0.89863.6937-0.4001-0.0424-0.1992-0.2641-0.5879-1.1023-0.11761.16120.98050.62320.21640.19661.47850.46651.227955.278354.5519-49.6601
53.92270.1607-1.21233.0494-0.40183.8452-0.09470.7799-0.0514-0.8966-0.3588-0.9270.5090.5070.37950.72020.05240.27160.950.14340.817343.812656.1999-63.6334
61.88640.6618-1.24332.2021-0.30452.0562-0.17370.1055-0.022-0.2247-0.01-0.24450.06680.35620.22410.44480.0382-0.00610.57250.05360.444322.592855.4253-45.4111
72.197-0.3407-0.40192.492-0.47823.7734-0.130.37150.49-0.01590.0415-0.5262-0.21130.98310.02550.357-0.02670.01260.65870.13670.605527.535166.3839-45.6686
82.89670.7003-0.27962.8554-0.34172.6804-0.10680.12830.4316-0.0212-0.0728-0.1827-0.40150.43630.12290.3738-0.0656-0.06910.4680.09440.492121.906271.0927-42.5265
94.22040.3572-0.43413.6006-1.3213.9326-0.1084-0.6695-0.09830.5247-0.1555-0.0684-0.07170.30270.22590.51080.0196-0.04850.42760.00480.429510.442557.1989-23.1263
103.4871-0.1791-2.28411.18280.36072.5059-0.21690.2105-0.0766-0.1808-0.0744-0.27020.07670.53050.26360.3952-0.0589-0.02580.6080.0520.510126.275560.7002-47.2912
116.26751.32030.3743.25130.88583.68610.2403-0.8360.57680.7723-0.27250.1057-0.28770.16140.00820.7257-0.066-0.0640.4484-0.07060.716917.79378.5488-34.436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 550 )
3X-RAY DIFFRACTION3chain 'B' and (resid 56 through 97 )
4X-RAY DIFFRACTION4chain 'B' and (resid 98 through 156 )
5X-RAY DIFFRACTION5chain 'B' and (resid 157 through 236 )
6X-RAY DIFFRACTION6chain 'B' and (resid 237 through 286 )
7X-RAY DIFFRACTION7chain 'B' and (resid 287 through 328 )
8X-RAY DIFFRACTION8chain 'B' and (resid 329 through 418 )
9X-RAY DIFFRACTION9chain 'B' and (resid 419 through 461 )
10X-RAY DIFFRACTION10chain 'B' and (resid 462 through 520 )
11X-RAY DIFFRACTION11chain 'B' and (resid 521 through 550 )

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