[English] 日本語
Yorodumi
- PDB-3vc3: Crystal structure of beta-cyanoalanine synthase K95A mutant in soybean -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vc3
TitleCrystal structure of beta-cyanoalanine synthase K95A mutant in soybean
Componentsbeta-cyanoalnine synthase
KeywordsTRANSFERASE / beta-cyanoalanine synthase
Function / homology
Function and homology information


L-3-cyanoalanine synthase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / mitochondrion / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C6P / Cysteine synthase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.766 Å
AuthorsYi, H. / Jez, J.M.
CitationJournal: Plant Cell / Year: 2012
Title: Structure of Soybean beta-Cyanoalanine Synthase and the Molecular Basis for Cyanide Detoxification in Plants.
Authors: Yi, H. / Juergens, M. / Jez, J.M.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: beta-cyanoalnine synthase
B: beta-cyanoalnine synthase
C: beta-cyanoalnine synthase
D: beta-cyanoalnine synthase
E: beta-cyanoalnine synthase
F: beta-cyanoalnine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,18412
Polymers223,0706
Non-polymers2,1146
Water32,6251811
1
A: beta-cyanoalnine synthase
B: beta-cyanoalnine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0614
Polymers74,3572
Non-polymers7052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-45 kcal/mol
Surface area22120 Å2
MethodPISA
2
C: beta-cyanoalnine synthase
D: beta-cyanoalnine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0614
Polymers74,3572
Non-polymers7052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-48 kcal/mol
Surface area22320 Å2
MethodPISA
3
E: beta-cyanoalnine synthase
hetero molecules

F: beta-cyanoalnine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0614
Polymers74,3572
Non-polymers7052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6510 Å2
ΔGint-45 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.092, 154.325, 198.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein
beta-cyanoalnine synthase


Mass: 37178.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Strain: Williams 82 / Gene: GLYMA09G39390, OAS-TL3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I1L6I6*PLUS, cysteine synthase
#2: Chemical
ChemComp-C6P / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE / 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM


Mass: 352.301 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H17N2O7PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1811 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLOCALIZATION PEPTIDE AT THE N-TERMINAL. NCBI SEQUENCE REFERENCE XP_003534555.1, RESIDUES 52-373

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG-3350, 0.2 M potassium citrate, pH 7.5, vapor diffusion, hanging drop, temperature 279K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.766→50 Å / Num. obs: 204348 / % possible obs: 96.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Χ2: 1.98 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.766-1.82.70.726102431.973198.2
1.8-1.833.20.783102892.115197.9
1.83-1.873.80.774102782.047197.9
1.87-1.9140.667102311.903197.5
1.91-1.9540.568102241.967197.4
1.95-1.994.10.496102132.157197.4
1.99-2.044.10.427102371.912197.2
2.04-2.14.10.354102351.987197.1
2.1-2.164.10.296101681.876196.9
2.16-2.234.10.251102211.89196.7
2.23-2.314.20.239101361.863196.5
2.31-2.44.20.205101421.854196.2
2.4-2.514.20.178101561.722196
2.51-2.644.20.152101421.725195.7
2.64-2.814.20.127101131.696195.5
2.81-3.034.20.105101771.821195.6
3.03-3.334.30.093102172.196195.8
3.33-3.814.30.079102542.817195.6
3.81-4.84.20.056102522.291195
4.8-504.20.049104201.81193

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.766→47.205 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8746 / SU ML: 0.39 / σ(F): 0 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 1891 0.94 %
Rwork0.17 --
obs0.1703 201382 94.24 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.836 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 87.84 Å2 / Biso mean: 21.9811 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.7328 Å2-0 Å2-0 Å2
2---2.4694 Å20 Å2
3----0.2635 Å2
Refinement stepCycle: LAST / Resolution: 1.766→47.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14564 0 132 1811 16507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715083
X-RAY DIFFRACTIONf_angle_d1.06320481
X-RAY DIFFRACTIONf_chiral_restr0.072365
X-RAY DIFFRACTIONf_plane_restr0.0052650
X-RAY DIFFRACTIONf_dihedral_angle_d12.075708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.766-1.81050.29041070.2857112601136775
1.8105-1.85950.28171110.2563126001271184
1.8595-1.91420.30021290.2208131871331688
1.9142-1.9760.25661310.1944137051383691
1.976-2.04660.23621310.1796139661409793
2.0466-2.12860.19141390.1683143071444695
2.1286-2.22540.19461390.1644146091474897
2.2254-2.34280.19191410.1612147161485798
2.3428-2.48950.19091410.1676148881502999
2.4895-2.68170.23151400.1687149641510499
2.6817-2.95160.2011430.17141510815251100
2.9516-3.37860.20791440.16861518915333100
3.3786-4.25620.16991460.14621532215468100
4.2562-47.22230.1731490.1572156701581999
Refinement TLS params.Method: refined / Origin x: -27.1296 Å / Origin y: 33.5823 Å / Origin z: 9.8301 Å
111213212223313233
T0.0625 Å2-0.0013 Å20.0031 Å2-0.0704 Å2-0.0009 Å2--0.0686 Å2
L0.0064 °20.0055 °20.0038 °2-0.0135 °20.0135 °2--0.0137 °2
S0.0097 Å °0.0064 Å °-0.0032 Å °0.0033 Å °-0.0002 Å °-0.0029 Å °-0.005 Å °0.0055 Å °0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 501
2X-RAY DIFFRACTION1allB23 - 501
3X-RAY DIFFRACTION1allC23 - 501
4X-RAY DIFFRACTION1allD22 - 501
5X-RAY DIFFRACTION1allE23 - 501
6X-RAY DIFFRACTION1allF23 - 501
7X-RAY DIFFRACTION1allD - C1 - 1866

+
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