[English] 日本語
Yorodumi
- PDB-8stx: Crystal structure of the F337A mutation of Trypanosoma cruzi gluc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8stx
TitleCrystal structure of the F337A mutation of Trypanosoma cruzi glucokinase in the apo form (open conformation)
ComponentsGlucokinase
KeywordsTRANSFERASE / glucokinase / mutation
Function / homologyGlucokinase / Glucokinase / membrane-bounded organelle / glucokinase activity / glucose binding / glycolytic process / ATPase, nucleotide binding domain / ATP binding / Glucokinase
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAbiskaroon, B. / Carey, S.M. / D'Antonio, E.L. / Chruszcz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochimie / Year: 2023
Title: At the outer part of the active site in Trypanosoma cruzi glucokinase: The role of phenylalanine 337.
Authors: Carey, S.M. / Kearns, S.P. / Millington, M.E. / Buechner, G.S. / Alvarez Jr., B.E. / Daneshian, L. / Abiskaroon, B. / Chruszcz, M. / D'Antonio, E.L.
History
DepositionMay 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase
B: Glucokinase


Theoretical massNumber of molelcules
Total (without water)84,3012
Polymers84,3012
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-30 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.307, 78.654, 77.079
Angle α, β, γ (deg.)90.000, 100.755, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: -2 - 365 / Label seq-ID: 12 - 379

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Glucokinase /


Mass: 42150.555 Da / Num. of mol.: 2 / Mutation: F337A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_114g48 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2WIH3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M Succinic Acid, 15% PEG3350, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 30375 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3 % / CC1/2: 0.982 / CC star: 0.996 / Rpim(I) all: 0.045 / Rrim(I) all: 0.081 / Net I/σ(I): 20.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1361 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.25 / Rrim(I) all: 0.43 / % possible all: 85.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.582 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.545 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.534 / ESU R Free: 0.274
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2446 1484 4.959 %
Rwork0.2023 28441 -
all0.204 --
obs-29925 96.33 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.306 Å2
Baniso -1Baniso -2Baniso -3
1-1.136 Å20 Å2-0.556 Å2
2---3.696 Å20 Å2
3---2.585 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5654 0 0 178 5832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125772
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165494
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.6437815
X-RAY DIFFRACTIONr_angle_other_deg0.4291.56412621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.628541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11510965
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.33310249
X-RAY DIFFRACTIONr_chiral_restr0.0570.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
X-RAY DIFFRACTIONr_nbd_refined0.2120.21271
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.25293
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22877
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.212
X-RAY DIFFRACTIONr_nbd_other0.1990.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2760.23
X-RAY DIFFRACTIONr_mcbond_it2.363.0882954
X-RAY DIFFRACTIONr_mcbond_other2.363.0882954
X-RAY DIFFRACTIONr_mcangle_it3.6295.5443689
X-RAY DIFFRACTIONr_mcangle_other3.6285.5453690
X-RAY DIFFRACTIONr_scbond_it2.7613.3172818
X-RAY DIFFRACTIONr_scbond_other2.763.3192819
X-RAY DIFFRACTIONr_scangle_it4.2785.9974126
X-RAY DIFFRACTIONr_scangle_other4.2775.9984127
X-RAY DIFFRACTIONr_lrange_it6.36329.4076476
X-RAY DIFFRACTIONr_lrange_other6.3629.3986466
X-RAY DIFFRACTIONr_ncsr_local_group_10.120.0511367
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.11950.05008
12AX-RAY DIFFRACTIONLocal ncs0.11950.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.3511090.30719550.3122760.9360.95190.68540.29
2.462-2.5290.3321080.26220770.26522170.9380.96398.55660.234
2.529-2.6020.2641010.24520020.24621320.9570.96798.63980.216
2.602-2.6820.293980.2419400.24321160.9430.95596.31380.205
2.682-2.770.239870.2119050.21120190.9590.97598.66270.184
2.77-2.8660.2861090.20718120.21119630.9450.97397.86040.181
2.866-2.9740.256790.20217880.20419210.9540.97497.1890.18
2.974-3.0950.27880.20116630.20418300.960.97695.68310.182
3.095-3.2310.242920.20416120.20617640.9620.97696.59860.188
3.231-3.3880.223750.20115870.20216770.970.97999.10550.188
3.388-3.570.273770.22614890.22916150.9610.94496.96590.209
3.57-3.7840.245800.21213830.21415050.9620.97597.20930.2
3.784-4.0430.239570.19812700.19914190.9560.93193.51660.18
4.043-4.3630.233750.16611920.1713290.9670.98395.33480.168
4.363-4.7740.17510.15810750.15812350.9810.98591.17410.164
4.774-5.3280.219670.18210340.18411140.9780.98498.8330.188
5.328-6.1330.176470.1959440.19410010.980.98399.0010.201
6.133-7.4670.291380.1927930.1978480.950.97997.99530.209
7.467-10.3770.198230.175700.1716620.9790.98289.5770.191
10.377-39.5820.27220.2183430.2214060.9690.97289.90150.233
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)
11.87940.22960.34175.9189-0.78493.1669-0.2344-0.22860.15440.70810.17980.2181-0.29240.2140.05460.14750.0333-0.01250.10010.00430.0338-0.155-14.43529.514
21.93790.0626-0.33543.249-0.64980.539-0.05220.0049-0.59240.06090.0527-0.03840.0441-0.0247-0.00050.0127-0.0185-0.0060.12190.02580.2309-19.467-9.50614.128
31.0309-0.2866-0.23891.15770.30411.4152-0.0458-0.2205-0.16250.240.0240.0534-0.0059-0.18010.02180.0599-0.02020.01130.25750.02030.1381-26.7313.14623.216
45.2685-1.8422-0.1695.1541-1.33594.02430.28550.20180.0731-0.9708-0.02710.34040.6922-0.4351-0.25840.2743-0.054-0.09690.08110.00180.0635-10.577-6.104-20.309
50.78240.0377-0.08221.6989-0.43961.05420.03980.07770.0156-0.0813-0.03410.01080.0390.0038-0.00570.0086-0.0034-0.01540.1988-0.01750.1833-11.00512.061-0.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA-2 - 132
2X-RAY DIFFRACTION2ALLA133 - 212
3X-RAY DIFFRACTION3ALLA213 - 367

+
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