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- PDB-7s2p: Crystal structure of the F337L mutation of Trypanosoma cruzi gluc... -

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Basic information

Entry
Database: PDB / ID: 7s2p
TitleCrystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN
ComponentsGlucokinase 1
KeywordsTRANSFERASE / Trypanosoma cruzi / Chagas disease
Function / homology
Function and homology information


glucokinase / glucokinase activity / glucose binding / glycolytic process / ATP binding
Similarity search - Function
Glucokinase / Glucokinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Chem-4UZ / Glucokinase 1, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 complex with inhibitor CBZ-GlcN
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1085
Polymers84,3852
Non-polymers7233
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-54 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.227, 78.951, 77.027
Angle α, β, γ (deg.)90.000, 94.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 365 / Label seq-ID: 15 - 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: Sugar ChemComp-4UZ / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-beta-D-glucopyranose / N-[(benzyloxy)carbonyl]-beta-D-glucosamine / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-beta-D-glucose / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-D-glucose / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 313.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: A ligand-free TcGlcK(F337L) crystal was soaked in 1.0 mM CBZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 15% (w/v) PEG 3,350 for 24 hours

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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: 2.35→40 Å / Num. obs: 33656 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/σ(I): 35.3
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1666 / CC1/2: 0.702 / Rpim(I) all: 0.372 / Rrim(I) all: 0.718 / % possible all: 98.2

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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: 2.35→38.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.396 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1679 5 %RANDOM
Rwork0.2015 ---
obs0.2041 31970 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.77 Å2 / Biso mean: 71.278 Å2 / Biso min: 40.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å21.31 Å2
2--2.15 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.35→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5627 0 49 52 5728
Biso mean--67.73 60.36 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135795
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175488
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6487848
X-RAY DIFFRACTIONr_angle_other_deg2.3531.57212603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2575732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73921.667288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97915964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3181541
X-RAY DIFFRACTIONr_chiral_restr0.0770.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026577
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021323
Refine LS restraints NCS

Ens-ID: 1 / Number: 11026 / 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: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 89 -
Rwork0.286 2210 -
all-2299 -
obs--92.55 %
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)
16.14410.7126-3.46262.83240.07214.62830.1254-1.2473-0.11910.8158-0.2006-0.37750.61450.52290.07530.6633-0.0684-0.13230.37960.04610.0608-21.276-6.3657.729
21.82820.7782-0.45282.14080.3551.64480.1431-0.04430.54740.0816-0.0890.3681-0.0173-0.1462-0.05420.2722-0.0111-0.02570.0183-0.00940.3555-26.01613.14838.197
34.34971.3526-0.66061.9020.53070.9235-0.4831.2990.0074-0.34670.31270.02740.2909-0.30590.17030.5676-0.18-0.0160.4216-0.02560.1113-28.573-11.40714.783
43.00910.7983-0.36262.08880.19971.5582-0.27420.76990.2592-0.48410.3347-0.35010.04330.1203-0.06050.4503-0.09290.03080.23350.05490.1945-9.8722.10515.257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2A130 - 366
3X-RAY DIFFRACTION3B1 - 215
4X-RAY DIFFRACTION4B216 - 367

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