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- PDB-8b9w: Cysteine Synthase from Trypanosoma theileri with PLP bound -

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Basic information

Entry
Database: PDB / ID: 8b9w
TitleCysteine Synthase from Trypanosoma theileri with PLP bound
ComponentsPutative cysteine synthase
KeywordsTRANSFERASE / Amino acid synthesis / Pyridoxal 5-phosphate
Function / homologyCysteine synthase CysK / Cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / PYRIDOXAL-5'-PHOSPHATE / Putative cysteine synthase
Function and homology information
Biological speciesTrypanosoma theileri (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSowerby, K.V. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis.
Authors: Sowerby, K. / Freitag-Pohl, S. / Murillo, A.M. / Silber, A.M. / Pohl, E.
History
DepositionOct 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: 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
A: Putative cysteine synthase
B: Putative cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,54910
Polymers75,5592
Non-polymers9908
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-46 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.303, 187.303, 187.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 24 - 349 / Label seq-ID: 24 - 349

Dom-ID
1
2

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

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Components

#1: Protein Putative cysteine synthase /


Mass: 37779.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma theileri (eukaryote) / Gene: TM35_000064350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X0P4R1
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.75→76.47 Å / Num. obs: 28493 / % possible obs: 100 % / Redundancy: 56.3 % / CC1/2: 0.997 / Net I/σ(I): 23.5
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 1434 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AIR

4air


Resolution: 2.75→76.466 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.881 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.357 / ESU R Free: 0.253
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2085 1448 5.085 %
Rwork0.1478 27027 -
all0.151 --
obs-28475 99.993 %
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: 65.938 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.75→76.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4827 0 61 141 5029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164682
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.6356787
X-RAY DIFFRACTIONr_angle_other_deg0.7141.54710888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4625666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.7981033
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45410815
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.81110188
X-RAY DIFFRACTIONr_chiral_restr0.0980.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
X-RAY DIFFRACTIONr_nbd_refined0.2230.21021
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.24537
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22427
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2140
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2880.25
X-RAY DIFFRACTIONr_nbd_other0.2030.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0350.21
X-RAY DIFFRACTIONr_mcbond_it9.7896.9472634
X-RAY DIFFRACTIONr_mcbond_other9.7896.9482634
X-RAY DIFFRACTIONr_mcangle_it12.82410.3763292
X-RAY DIFFRACTIONr_mcangle_other12.82310.3773293
X-RAY DIFFRACTIONr_scbond_it11.687.3562360
X-RAY DIFFRACTIONr_scbond_other11.6787.3572361
X-RAY DIFFRACTIONr_scangle_it14.84410.7633489
X-RAY DIFFRACTIONr_scangle_other14.84210.7643490
X-RAY DIFFRACTIONr_lrange_it16.20983.9845283
X-RAY DIFFRACTIONr_lrange_other16.18883.9785278
X-RAY DIFFRACTIONr_ncsr_local_group_10.1330.059267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.133440.05007
12AX-RAY DIFFRACTIONLocal ncs0.133440.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.75-2.8220.3111180.29419250.29520430.9520.9590.282
2.822-2.8990.3011170.22819410.23220580.9470.9720.205
2.899-2.9830.25940.19818890.219830.9520.9750.172
2.983-3.0740.273980.17618190.18119170.9440.980.149
3.074-3.1750.243910.17217720.17518630.9520.9810.143
3.175-3.2860.247850.15917100.16417950.960.9840.131
3.286-3.410.1921040.1616440.16217480.9740.9840.137
3.41-3.5490.2181020.16715910.17116930.9660.9840.143
3.549-3.7070.247810.15315230.15816040.9690.9870.129
3.707-3.8870.209560.14914960.15115520.9640.9860.124
3.887-4.0970.2790.14213620.14514410.9770.9880.12
4.097-4.3440.185570.11613470.11914040.9760.9920.098
4.344-4.6430.203610.1112600.11313210.9750.9930.092
4.643-5.0140.136570.09811580.112150.9870.9940.082
5.014-5.490.151600.10610770.10911370.9850.9930.09
5.49-6.1340.193460.139750.13210210.9780.990.107
6.134-7.0750.206470.1418720.1449190.9790.9880.116
7.075-8.6470.169490.1397300.1417790.9830.9880.123
8.647-12.1510.213330.1315790.1356120.9730.9890.123
12.151-76.4660.225130.2663570.2643700.9770.9540.247

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