[English] 日本語
Yorodumi
- PDB-7s2n: Crystal structure of the F337L mutation of Trypanosoma cruzi gluc... -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: 0 / 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: 0 / Auth seq-ID: 0 - 365 / Label seq-ID: 14 - 379

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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more