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- PDB-8b9m: Cysteine Synthase from Leishmania Infantum -

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Basic information

Entry
Database: PDB / ID: 8b9m
TitleCysteine Synthase from Leishmania Infantum
ComponentsCysteine synthase
KeywordsUNKNOWN FUNCTION / Cysteine synthase / Amino acid synthesis / Leishmaniasis
Function / homologyCysteine synthase CysK / cysteine synthase / 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 / Cysteine synthase
Function and homology information
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 6, 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1477
Polymers74,8562
Non-polymers2915
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-87 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.879, 87.759, 138.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine synthase /


Mass: 37427.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ_36_3750 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ID39, cysteine synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium Chloride, Bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→87.77 Å / Num. obs: 60590 / % possible obs: 99.6 % / Redundancy: 11.8 % / CC1/2: 0.991 / Net I/σ(I): 11.96
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 2908 / CC1/2: 0.805

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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: 1.75→74.175 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.847 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.108 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2052 3030 5.007 %
Rwork0.1641 57490 -
all0.166 --
obs-60520 99.554 %
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: 23.883 Å2
Baniso -1Baniso -2Baniso -3
1--0.126 Å2-0 Å2-0 Å2
2---0.665 Å20 Å2
3---0.791 Å2
Refinement stepCycle: LAST / Resolution: 1.75→74.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 15 404 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124747
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164558
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.6326471
X-RAY DIFFRACTIONr_angle_other_deg0.5071.55110645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.9741024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78310840
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.67910176
X-RAY DIFFRACTIONr_chiral_restr0.0730.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined0.2350.2920
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24269
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22409
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2341
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.210
X-RAY DIFFRACTIONr_nbd_other0.20.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it2.4322.4472492
X-RAY DIFFRACTIONr_mcbond_other2.4262.4472492
X-RAY DIFFRACTIONr_mcangle_it3.8013.6463122
X-RAY DIFFRACTIONr_mcangle_other3.83.6473123
X-RAY DIFFRACTIONr_scbond_it3.2272.7652255
X-RAY DIFFRACTIONr_scbond_other3.2272.7652256
X-RAY DIFFRACTIONr_scangle_it4.9673.9993321
X-RAY DIFFRACTIONr_scangle_other4.96643322
X-RAY DIFFRACTIONr_lrange_it7.11136.2455367
X-RAY DIFFRACTIONr_lrange_other7.06734.2395266
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
1.75-1.7950.292330.28641800.28744270.9350.93599.68380.273
1.795-1.8450.2472100.25240360.25243010.9530.9598.72120.234
1.845-1.8980.2472110.21939640.22142270.9570.96398.76980.194
1.898-1.9560.2521780.19938720.20140890.9520.97199.04620.173
1.956-2.0210.2192190.18237420.18439620.9690.97799.97480.154
2.021-2.0910.2131660.17436470.17638460.9680.97999.1420.147
2.091-2.170.2181990.16734590.1736800.970.98299.40220.142
2.17-2.2590.2021840.15633820.15935840.9770.98499.49780.133
2.259-2.3590.1991610.14832700.1534450.9760.98699.59360.123
2.359-2.4740.1831630.14331220.14532950.9780.98799.69650.12
2.474-2.6080.2141660.15329510.15631230.9720.98599.80790.129
2.608-2.7660.2071540.1628280.16329860.9720.98499.8660.137
2.766-2.9570.2071340.16226590.16427950.9720.98399.92840.14
2.957-3.1930.2121400.15424870.15726280.9720.98499.96190.139
3.193-3.4970.2041160.16923160.1724320.9720.9831000.155
3.497-3.9090.206910.15320970.15521880.9730.9861000.143
3.909-4.5110.161960.1318750.13219710.9850.991000.128
4.511-5.520.176890.14315980.14416870.9880.991000.142
5.52-7.7850.212720.17512540.17713260.9780.9841000.172
7.785-74.1750.188480.1557510.1577990.9790.9831000.173

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