[English] 日本語
Yorodumi
- PDB-3k25: Crystal Structure of Slr1438 protein from Synechocystis sp. PCC 6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k25
TitleCrystal Structure of Slr1438 protein from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR112
ComponentsSlr1438 protein
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / SgR112 / P73504_SYNY3
Function / homology
Function and homology information


glucose-6-phosphate 1-epimerase activity / carbohydrate binding / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Slr1438 protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.551 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target SgR112
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Slr1438 protein
B: Slr1438 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5955
Polymers66,3102
Non-polymers2853
Water21612
1
A: Slr1438 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2502
Polymers33,1551
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Slr1438 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3453
Polymers33,1551
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.566, 145.566, 60.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Slr1438 protein


Mass: 33154.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: slr1438 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P73504
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: PEG-8K 20%, Nh4H2Po4, n-Butanol 0.7%, 2,2,2-Trifluororthanol 4.0%, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 46233 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.1
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.3

-
Processing

Software
NameVersionClassificationNB
PHENIX1.4_115refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.551→47.648 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1219 5.13 %
Rwork0.2326 --
obs0.2331 23776 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.903 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 45.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.5795 Å20 Å20 Å2
2---1.5795 Å2-0 Å2
3---3.159 Å2
Refinement stepCycle: LAST / Resolution: 2.551→47.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 15 12 4705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074824
X-RAY DIFFRACTIONf_angle_d1.3946568
X-RAY DIFFRACTIONf_dihedral_angle_d22.4281738
X-RAY DIFFRACTIONf_chiral_restr0.097686
X-RAY DIFFRACTIONf_plane_restr0.008872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5512-2.65340.35911350.33792533X-RAY DIFFRACTION100
2.6534-2.77410.36081330.32592531X-RAY DIFFRACTION100
2.7741-2.92040.35151240.30722570X-RAY DIFFRACTION100
2.9204-3.10330.26771350.28442520X-RAY DIFFRACTION100
3.1033-3.34280.30611540.27572517X-RAY DIFFRACTION100
3.3428-3.67910.26141160.252180X-RAY DIFFRACTION86
3.6791-4.21120.21571460.21222488X-RAY DIFFRACTION98
4.2112-5.30460.15921330.15062584X-RAY DIFFRACTION100
5.3046-47.65590.19091430.18352634X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -60.1731 Å / Origin y: 2.0517 Å / Origin z: 1.1287 Å
111213212223313233
T0.144 Å2-0.0481 Å2-0.0227 Å2-0.1841 Å2-0.0198 Å2--0.1007 Å2
L0.5127 °20.5133 °2-0.2383 °2-0.7683 °2-0.2429 °2---0.0737 °2
S0.0122 Å °0.0338 Å °-0.0344 Å °0.0291 Å °0.0045 Å °-0.1196 Å °-0.0474 Å °-0.0758 Å °0.0091 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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