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- PDB-6xo2: Structural Characterization of Beta Cyanoalanine Synthase from Te... -

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Basic information

Entry
Database: PDB / ID: 6xo2
TitleStructural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae (two-spotted spider mite)
ComponentsBeta-cyanoalanine synthase
KeywordsBIOSYNTHETIC PROTEIN / Beta Cyanoalanine Synthase / PLP. two-spotted spider mite
Function / homologycysteine biosynthetic process / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / Beta-cyanoalanine synthase
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDaneshian, L. / Schlachter, C. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)2020-67014-31179 United States
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Structural and functional characterization of beta-cyanoalanine synthase from Tetranychus urticae.
Authors: Daneshian, L. / Renggli, I. / Hanaway, R. / Offermann, L.R. / Schlachter, C.R. / Hernandez Arriaza, R. / Henry, S. / Prakash, R. / Wybouw, N. / Dermauw, W. / Shimizu, L.S. / Van Leeuwen, T. ...Authors: Daneshian, L. / Renggli, I. / Hanaway, R. / Offermann, L.R. / Schlachter, C.R. / Hernandez Arriaza, R. / Henry, S. / Prakash, R. / Wybouw, N. / Dermauw, W. / Shimizu, L.S. / Van Leeuwen, T. / Makris, T.M. / Grbic, V. / Grbic, M. / Chruszcz, M.
History
DepositionJul 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-cyanoalanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8233
Polymers34,5171
Non-polymers3062
Water5,224290
1
A: Beta-cyanoalanine synthase
hetero molecules

A: Beta-cyanoalanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6476
Polymers69,0352
Non-polymers6124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5430 Å2
ΔGint-34 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.376, 64.376, 143.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

21A-959-

HOH

31A-1072-

HOH

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Components

#1: Protein Beta-cyanoalanine synthase


Mass: 34517.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107363798 / Plasmid: pMCSG35 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1KF23
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Ammonium Chloride, 12% PEG 3350, pH 7.0.

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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: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 40447 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Rsym value: 0.079 / Net I/av σ(I): 33.5 / Net I/σ(I): 41.05
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1971 / CC1/2: 0.757 / CC star: 0.928 / Rpim(I) all: 0.335 / Rrim(I) all: 0.763 / Rsym value: 0.681 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6pmu

6pmu


Resolution: 1.6→38.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.522 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 1918 4.8 %RANDOM
Rwork0.1645 ---
obs0.1656 38452 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.15 Å2 / Biso mean: 29.786 Å2 / Biso min: 18.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2--0.33 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 1.6→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 19 290 2492
Biso mean--33.61 46.37 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132256
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172102
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.6453058
X-RAY DIFFRACTIONr_angle_other_deg2.461.5754893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46623.64696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8621510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022534
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02427
LS refinement shellResolution: 1.601→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 112 -
Rwork0.234 2793 -
all-2905 -
obs--99.01 %
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)
10.37150.30170.07750.7308-0.04270.4865-0.00220.0823-0.05870.01020.018-0.05840.0409-0.0814-0.01580.01-0.01050.00020.0503-0.01030.009726.909719.515532.3287
20.16020.136-0.08961.2168-0.44320.883-0.03360.0955-0.0074-0.07560.08270.07090.019-0.1894-0.04920.0221-0.0044-0.00810.12030.0090.018321.22826.952919.1262
31.06790.2130.14630.96990.05991.672-0.01530.1913-0.0367-0.10830.046-0.0821-0.00880.0914-0.03070.03030.00040.01290.074-0.00980.008637.436731.957617.4182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 151
2X-RAY DIFFRACTION2A152 - 222
3X-RAY DIFFRACTION3A256 - 319

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