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- PDB-7s2n: Crystal structure of the F337L mutation of Trypanosoma cruzi gluc... -

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Basic information

Entry
Database: PDB / ID: 7s2n
TitleCrystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in the apo form (open conformation)
ComponentsGlucokinase 1
KeywordsTRANSFERASE / Trypanosoma cruzi / Chagas disease
Function / homologyGlucokinase / Glucokinase / glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATPase, nucleotide binding domain / ATP binding / Glucokinase 1, putative
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCarey, S.M. / Nettles, R.B. / Daneshian, L. / Chruszcz, M. / D'Antonio, E.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentUniversity of South Carolina, Office of the Vice President for Research, Magellan Program United States
CitationJournal: To Be Published
Title: Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in the apo form (open conformation)
Authors: Carey, S.M. / Nettles, R.B. / Daneshian, L. / Chruszcz, M. / D'Antonio, E.L.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase 1
B: Glucokinase 1


Theoretical massNumber of molelcules
Total (without water)84,3852
Polymers84,3852
Non-polymers00
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-31 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.750, 78.985, 77.567
Angle α, β, γ (deg.)90.000, 101.170, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 0 - 365 / Label seq-ID: 14 - 379

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glucokinase 1


Mass: 42192.633 Da / Num. of mol.: 2 / Mutation: F337L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053510187.100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E4E1, glucokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0 uL of 7.4 mg/mL TcGlcK(F337L) in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium ...Details: 1.0 uL of 7.4 mg/mL TcGlcK(F337L) in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium citrate tribasic] was equilibrated against 85 uL of the precipitant solution using a 96-well sitting-drop plate (Innovadyne)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 80560 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 32.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4061 / CC1/2: 0.688 / Rpim(I) all: 0.4 / Rrim(I) all: 0.774 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2R

2q2r


Resolution: 1.75→39.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.47 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 3956 4.9 %RANDOM
Rwork0.1607 ---
obs0.1622 76581 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.3 Å2 / Biso mean: 34.491 Å2 / Biso min: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.42 Å2
2---0.24 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.75→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5675 0 0 729 6404
Biso mean---44.3 -
Num. residues----736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135819
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175572
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.6377878
X-RAY DIFFRACTIONr_angle_other_deg2.3161.57312815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84821.803294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94815994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4061541
X-RAY DIFFRACTIONr_chiral_restr0.0910.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026659
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021339
Refine LS restraints NCS

Ens-ID: 1 / Number: 11256 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.75→1.794 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.273 274 -
Rwork0.244 5294 -
obs--92.49 %
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)
11.4118-1.06620.75270.9645-0.51280.9801-0.0756-0.0597-0.11140.15490.09290.1659-0.01070.0418-0.01730.138-0.0260.05250.07160.01670.11146.071-8.476100.608
20.7893-0.193-0.1710.76590.13370.7016-0.0198-0.1668-0.15170.1113-0.00880.12430.0169-0.12070.02850.0454-0.03970.03710.1219-0.00030.120626.2388.03398.749
36.1108-0.4698-1.43422.63710.00943.4217-0.14690.07840.0342-0.46860.12820.2670.4746-0.25260.01870.2465-0.0185-0.050.04130.00730.054441.602-2.64856.464
40.82240.10310.00551.373-0.20160.79360.08210.06680.0165-0.0896-0.05370.0463-0.03310.0429-0.02840.02250.00510.01690.0581-0.02590.07841.72218.77976.226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 202
2X-RAY DIFFRACTION2A203 - 367
3X-RAY DIFFRACTION3B0 - 133
4X-RAY DIFFRACTION4B134 - 366

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