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- PDB-8u2w: Glucose-6-phosphate 1-dehydrogenase (G6PDH) from Crithidia fascic... -

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Basic information

Entry
Database: PDB / ID: 8u2w
TitleGlucose-6-phosphate 1-dehydrogenase (G6PDH) from Crithidia fasciculata (NADP bound)
ComponentsAcetyl-coenzyme A synthetase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / 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 DirectorS10OD030394 United States
CitationJournal: To be published
Title: Glucose-6-phosphate 1-dehydrogenase (G6PDH) from Crithidia fasciculata (NADP bound)
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 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: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9004
Polymers154,4132
Non-polymers1,4872
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-26 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.332, 123.258, 162.171
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 Acetyl-coenzyme A synthetase


Mass: 77206.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Plasmid: CrfaA.01031.a.HZ1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Berkeley H8: 30% (w/v) PEG 4000, 100 mM Sodium acetate / Hydrochloric acid pH 4.6, 200 mM Ammonium acetate. CrfaA.01031.a.HZ1.PW39196 at 19.7 mg/mL. plate 13383 well H8 drop 2. Puck: PSL- ...Details: Berkeley H8: 30% (w/v) PEG 4000, 100 mM Sodium acetate / Hydrochloric acid pH 4.6, 200 mM Ammonium acetate. CrfaA.01031.a.HZ1.PW39196 at 19.7 mg/mL. plate 13383 well H8 drop 2. Puck: PSL-1713, Cryo: Direct. 2mM NADPH and BG6 added prior to crystallization. No BG6 bound and NADPH is partially disordered.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 8, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→86.47 Å / Num. obs: 50896 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.033 / Rrim(I) all: 0.121 / Χ2: 1 / Net I/σ(I): 13.7 / Num. measured all: 694617
Reflection shellResolution: 2.35→2.41 Å / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 1.911 / Num. measured all: 49526 / Num. unique obs: 3733 / CC1/2: 0.705 / Rpim(I) all: 0.544 / Rrim(I) all: 1.988 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→33.87 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 2524 4.97 %
Rwork0.215 --
obs0.2167 50792 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 62 55 7642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047752
X-RAY DIFFRACTIONf_angle_d0.71510503
X-RAY DIFFRACTIONf_dihedral_angle_d12.4152865
X-RAY DIFFRACTIONf_chiral_restr0.0461156
X-RAY DIFFRACTIONf_plane_restr0.0051354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.38491240.34462668X-RAY DIFFRACTION100
2.4-2.440.33721560.31992618X-RAY DIFFRACTION100
2.44-2.50.35541480.29282649X-RAY DIFFRACTION100
2.5-2.560.3341390.27682669X-RAY DIFFRACTION100
2.56-2.620.28761160.26342696X-RAY DIFFRACTION100
2.62-2.690.3031760.25512601X-RAY DIFFRACTION100
2.69-2.770.30911130.27252669X-RAY DIFFRACTION100
2.77-2.860.30741190.27072695X-RAY DIFFRACTION100
2.86-2.960.29661560.28052668X-RAY DIFFRACTION100
2.96-3.080.29831230.26252686X-RAY DIFFRACTION100
3.08-3.220.29111230.2662671X-RAY DIFFRACTION100
3.22-3.390.29941550.24982654X-RAY DIFFRACTION100
3.39-3.60.30041340.23282718X-RAY DIFFRACTION100
3.6-3.880.26971450.21162660X-RAY DIFFRACTION100
3.88-4.270.20571310.17672718X-RAY DIFFRACTION100
4.27-4.880.17031580.14912686X-RAY DIFFRACTION100
4.89-6.150.22051430.1932755X-RAY DIFFRACTION100
6.15-33.870.21191650.18592787X-RAY DIFFRACTION99
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)
15.2181-0.3732-0.6856.40612.91756.77270.1284-0.25070.21020.3213-0.1456-0.18130.23740.034-0.03850.7606-0.0518-0.04480.57960.00790.30671.413648.86418.0077
20.7603-0.4976-0.16541.10920.45743.13790.0825-0.415-0.21421.31580.112-0.08720.77690.4872-0.11631.12810.1736-0.15750.70160.09780.4844.651638.566616.6766
30.66430.1725-0.18631.43661.27262.8194-0.0343-0.3457-0.09580.5183-0.26540.09860.7941-0.33330.32050.7014-0.02650.06340.53660.04220.4114-5.867839.0773-2.7668
41.61440.3663-0.49681.2893-0.57032.0692-0.233-0.3395-0.30270.219-0.0204-0.09340.80910.16930.16250.82570.11210.08310.37550.04860.45455.016329.1635-21.4373
57.32791.1826-3.50094.2509-2.06018.952-0.2058-0.0145-0.7352-0.2683-0.2357-0.60010.30141.10960.52830.52270.09380.01650.55420.06180.578322.542743.0394-31.3409
61.3901-0.2199-0.22831.9529-0.20632.5235-0.1441-0.1417-0.4251-0.1478-0.1064-0.08790.83220.1570.10640.87710.11410.15940.3980.13490.5662-0.226328.2006-16.0145
73.4474-0.0506-0.04541.9742-0.66523.3105-0.4971-0.3204-0.7262-0.5764-0.6289-0.9080.6151.26520.76440.55830.2050.34761.11920.40611.212751.943151.4369-52.1848
81.62310.3678-0.98021.5172-0.54661.9936-0.0804-0.05270.0137-0.0602-0.0718-0.2742-0.13890.38620.06670.3949-0.0468-0.04260.43890.03040.396524.656563.0187-44.1391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 139 )
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 328 )
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 442 )
5X-RAY DIFFRACTION5chain 'A' and (resid 443 through 481 )
6X-RAY DIFFRACTION6chain 'A' and (resid 482 through 550 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 172 )
8X-RAY DIFFRACTION8chain 'B' and (resid 173 through 549 )

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