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- PDB-4air: Leishmania major cysteine synthase -

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Basic information

Entry
Database: PDB / ID: 4air
TitleLeishmania major cysteine synthase
Components
  • Cysteine synthase
  • FGA-FGA-FGA-FGA
  • FGA-FGA-FGA-FGA-FGA
KeywordsTRANSFERASE
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeishmania major (eukaryote)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFyfe, P.K. / Westrop, G.D. / Coombs, G.H. / Hunter, W.N.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Leishmania Major Cysteine Synthase.
Authors: Fyfe, P.K. / Westrop, G.D. / Ramos, T. / Muller, S. / Coombs, G.H. / Hunter, W.N.
#1: Journal: Biochem.J. / Year: 2009
Title: Two Pathways for Cysteine Biosynthesis in Leishmania Major.
Authors: Williams, R.A.M. / Westrop, G.D. / Coombs, G.H.
History
DepositionFeb 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Jul 18, 2012Group: Database references
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Feb 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
C: FGA-FGA-FGA-FGA-FGA
D: FGA-FGA-FGA-FGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0766
Polymers77,0054
Non-polymers712
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.958, 86.325, 134.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6852, 0.6944, 0.22), (0.6931, -0.7144, 0.0962), (0.224, 0.08656, -0.9707)
Vector: -4.35, 1.137, 28.51)

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Components

#1: Protein Cysteine synthase /


Mass: 37903.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_36_3590 / Plasmid: PET15BTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q159, cysteine synthase
#2: Protein/peptide FGA-FGA-FGA-FGA-FGA


Mass: 663.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Protein/peptide FGA-FGA-FGA-FGA


Mass: 534.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPOLYGLUTAMIC ACID FORMED FROM FGA RESIDUES: THE RESOLVED HETEROGEN IS PART OF A MUCH LONGER POLYMER ...POLYGLUTAMIC ACID FORMED FROM FGA RESIDUES: THE RESOLVED HETEROGEN IS PART OF A MUCH LONGER POLYMER WITH A MASS OF FOUR HUNDRED KDA.
Sequence detailsINCLUDES HEXA-HIS TAG AND TEV CLEAVAGE SITE

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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: 2.02 Å3/Da / Density % sol: 34.15 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→48.9 Å / Num. obs: 53553 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHS

2bhs


Resolution: 1.8→45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.772 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20826 2712 5.1 %RANDOM
Rwork0.15663 ---
obs0.15921 50629 99.66 %-
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 mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.52 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 75 700 5347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225326
X-RAY DIFFRACTIONr_bond_other_d0.0010.023608
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9917259
X-RAY DIFFRACTIONr_angle_other_deg0.93838912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61624.518197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77715963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7841532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216177
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021023
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 185 -
Rwork0.209 3421 -
obs--99.89 %

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