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- PDB-7mfj: Structural Characterization of Beta Cyanoalanine Synthase from Te... -

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Basic information

Entry
Database: PDB / ID: 7mfj
TitleStructural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae
ComponentsBeta-cyanoalanine synthase
KeywordsSTRUCTURAL 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: 2.351 Å
AuthorsDaneshian, L. / Schlachter, C. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
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
DepositionApr 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-cyanoalanine synthase
BBB: Beta-cyanoalanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3916
Polymers68,7782
Non-polymers6124
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-34 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.801, 91.801, 140.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 0 - 318 / Label seq-ID: 1 - 319

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Beta-cyanoalanine synthase


Mass: 34389.168 Da / Num. of mol.: 2
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


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 42.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Sodium malonate pH 6, 12% PEG 3350

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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: Feb 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 25330 / % possible obs: 99.1 % / Redundancy: 11.5 % / CC1/2: 0.941 / CC star: 0.985 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.127 / Rsym value: 0.098 / Net I/σ(I): 17.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 5 / Num. unique obs: 1249 / CC1/2: 0.941 / CC star: 0.985 / Rpim(I) all: 0.147 / Rrim(I) all: 0.472 / Rsym value: 0.42 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PMU

6pmu


Resolution: 2.351→39.403 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.257 / SU ML: 0.171 / Cross valid method: FREE R-VALUE / ESU R: 0.453 / ESU R Free: 0.246
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2239 1245 5.029 %
Rwork0.1708 23513 -
all0.173 --
obs-24758 96.598 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.933 Å2
Baniso -1Baniso -2Baniso -3
1--1.951 Å20 Å20 Å2
2---1.951 Å20 Å2
3---3.901 Å2
Refinement stepCycle: LAST / Resolution: 2.351→39.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 38 277 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134668
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174417
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6446331
X-RAY DIFFRACTIONr_angle_other_deg1.3061.57810200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52923.805205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37815776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2891520
X-RAY DIFFRACTIONr_chiral_restr0.070.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02991
X-RAY DIFFRACTIONr_nbd_refined0.1910.2900
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24059
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22283
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1680.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.23
X-RAY DIFFRACTIONr_nbd_other0.2530.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0490.25
X-RAY DIFFRACTIONr_mcbond_it2.5953.592432
X-RAY DIFFRACTIONr_mcbond_other2.5913.5892430
X-RAY DIFFRACTIONr_mcangle_it3.8915.3723034
X-RAY DIFFRACTIONr_mcangle_other3.8915.3733035
X-RAY DIFFRACTIONr_scbond_it3.1313.8842236
X-RAY DIFFRACTIONr_scbond_other3.1313.8842237
X-RAY DIFFRACTIONr_scangle_it4.8735.73297
X-RAY DIFFRACTIONr_scangle_other4.8725.73298
X-RAY DIFFRACTIONr_lrange_it6.51742.0195121
X-RAY DIFFRACTIONr_lrange_other6.48941.9555085
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.058848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.083530.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.083530.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.351-2.4120.301920.2616460.26218620.8560.87193.34050.23
2.412-2.4780.286900.2117070.21417970.8820.921000.182
2.478-2.5490.228790.19216760.19417550.8930.9271000.164
2.549-2.6270.273920.19216130.19717050.9190.9281000.163
2.627-2.7130.255860.18215760.18616630.9140.93999.93990.158
2.713-2.8080.203790.15615210.15916020.9310.95599.87520.136
2.808-2.9130.234670.18314510.18515280.9170.94199.34560.162
2.913-3.0310.279820.17314130.17915220.9130.94698.2260.156
3.031-3.1650.219720.18213790.18414510.940.951000.165
3.165-3.3190.235660.18612980.18913660.9220.93999.85360.172
3.319-3.4970.241670.19112590.19413280.9290.94399.84940.177
3.497-3.7070.224630.16411850.16712510.9470.96299.76020.156
3.707-3.9610.203560.14811140.15111780.9530.9799.32090.145
3.961-4.2740.178520.15710020.15811110.9560.96594.86950.155
4.274-4.6770.235390.1519430.15310410.9410.96894.33240.149
4.677-5.220.189520.1517880.1549210.960.96791.20520.142
5.22-6.010.256390.1686670.1738480.9380.96183.25470.155
6.01-7.3180.191280.1495450.1517310.970.97178.38580.144
7.318-10.1750.135260.1184520.1185850.9770.98481.70940.121
10.175-39.4030.176180.1762780.1763760.9750.97478.72340.18

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