[English] 日本語
Yorodumi
- PDB-4fey: An X-ray Structure of a Putative Phosphogylcerate Kinase with Bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fey
TitleAn X-ray Structure of a Putative Phosphogylcerate Kinase with Bound ADP from Francisella tularensis subsp. tularensis SCHU S4
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: An X-ray Structure of a Putative Phosphogylcerate Kinase with Bound ADP from Francisella tularensis subsp. tularensis SCHU S4
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6852
Polymers42,2581
Non-polymers4271
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.616, 66.616, 206.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Phosphoglycerate kinase


Mass: 42257.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_1367c, pgk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q5NF76, phosphoglycerate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG3350, 50mM ADA pH7,ADP 1mM, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2011 / Details: Be Lenses
RadiationMonochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 19816 / Num. obs: 19816 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 68.59 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 32.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.66 / Num. unique all: 984 / % possible all: 100

-
Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHASERphasing
PHENIXmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EHJ
Resolution: 2.3→27.99 Å / Cor.coef. Fo:Fc: 0.9618 / Cor.coef. Fo:Fc free: 0.9407 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1013 5.12 %RANDOM
Rwork0.1932 ---
all0.1959 ---
obs0.1959 19788 --
Displacement parametersBiso mean: 82.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.0612 Å20 Å20 Å2
2---1.0612 Å20 Å2
3---2.1224 Å2
Refine analyzeLuzzati coordinate error obs: 0.496 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 27 117 3092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013032HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14103HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1429SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it3003HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_chiral_improper_torsion416SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3476SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3356 152 5.27 %
Rwork0.255 2734 -
all0.2591 2886 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.33094.39396.271911.4653.2271.4615-0.0909-0.0310.7692-0.1242-0.0673-0.3039-0.4726-0.08980.1582-0.2186-0.45590.2236-0.1499-0.45350.60524.386189.2292-35.4951
23.2224-2.4557-1.84346.98170.77962.87670.20410.62811.143-1.54650.3988-0.364-0.8012-0.17-0.60290.0889-0.31320.2788-0.31710.1279-0.187813.125482.5935-48.314
305.75730.51754.8323-1.36683.73920.13170.3514-0.4093-0.35420.17660.4297-0.0053-0.2937-0.30830.283-0.38890.17750.1006-0.0348-0.38118.955563.1696-50.4746
46.30781.3952-3.50532.90170.59784.7542-0.01531.39031.0832-1.17860.2992-0.4868-0.4386-0.0872-0.28390.1712-0.31980.25670.13270.1679-0.13616.711676.6005-53.6919
52.2946-1.59291.65370.04960.69832.6319-0.01090.1496-0.1629-0.11730.0748-0.42450.37020.38-0.0639-0.1226-0.08280.13760.0188-0.2001-0.0422.770665.1128-39.6819
67.0082-3.5899-3.25442.52721.6863.4397-0.0385-0.37111.24-0.28550.5441-0.9285-0.43920.6774-0.5055-0.1402-0.24290.0746-0.0574-0.18040.11117.826479.2392-36.0791
73.164-2.3453-0.4975.31610.50092.9093-0.5717-0.69070.06190.70170.47470.2407-0.0135-0.19760.097-0.07530.1192-0.00330.0228-0.0692-0.2802-7.998378.7079-18.7336
83.6793-1.4270.71082.732-1.61561.3234-0.1464-0.8669-0.31571.28450.1257-0.0351-0.4985-0.22030.02070.32410.16720.13340.25970.0724-0.2948-9.015971.8544-11.8986
95.25240.23390.10195.76271.07082.388-0.418-0.13420.7144-0.230.19210.8826-0.4387-0.51550.2259-0.15320.0875-0.1461-0.1187-0.0407-0.1327-13.586684.7656-26.8941
1000.51264.93200.488700.0499-0.53180.1832-0.02180.2377-0.651-0.20.0244-0.2876-0.1891-0.0865-0.0090.084-0.29250.194121.492578.5103-28.0729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 12}A1 - 12
2X-RAY DIFFRACTION2{A|13 - 61}A13 - 61
3X-RAY DIFFRACTION3{A|62 - 71}A62 - 71
4X-RAY DIFFRACTION4{A|72 - 118}A72 - 118
5X-RAY DIFFRACTION5{A|119 - 128}A119 - 128
6X-RAY DIFFRACTION6{A|129 - 176}A129 - 176
7X-RAY DIFFRACTION7{A|177 - 234}A177 - 234
8X-RAY DIFFRACTION8{A|235 - 251}A235 - 251
9X-RAY DIFFRACTION9{A|252 - 378}A252 - 378
10X-RAY DIFFRACTION10{A|379 - 392}A379 - 392

+
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