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- PDB-3vc3: Crystal structure of beta-cyanoalanine synthase K95A mutant in soybean -

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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


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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