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- PDB-3iqg: Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide... -

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Basic information

Entry
Database: PDB / ID: 3iqg
TitleStructure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNWNI
Components
  • Cysteine synthase
  • MNWNI
KeywordsTRANSFERASE / PROTEIN-PEPTIDE COMPLEX / Allosteric enzyme / Amino-acid biosynthesis / Cysteine biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoderick, S.L.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Design of o-acetylserine sulfhydrylase inhibitors by mimicking nature.
Authors: Salsi, E. / Bayden, A.S. / Spyrakis, F. / Amadasi, A. / Campanini, B. / Bettati, S. / Dodatko, T. / Cozzini, P. / Kellogg, G.E. / Cook, P.F. / Roderick, S.L. / Mozzarelli, A.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Cysteine synthase
P: MNWNI


Theoretical massNumber of molelcules
Total (without water)34,3282
Polymers34,3282
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-5 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.474, 112.474, 45.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cysteine synthase / CSase / O-acetylserine sulfhydrylase / O-acetylserine (thiol)-lyase / OAS-TL


Mass: 33651.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: cysK, HI1103 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase
#2: Protein/peptide MNWNI


Mass: 676.784 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: CAPS, Ammonium Sulfate, Lithium Sulfate, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 29, 2009
RadiationMonochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.04 Å / Num. all: 22692 / Num. obs: 22692 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 31.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 8.6 / Num. unique all: 3133 / % possible all: 95.7

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Processing

Software
NameClassification
StructureStudiodata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y7L

1y7l


Resolution: 1.9→28.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.719 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20534 1127 5 %RANDOM
Rwork0.16634 ---
all0.16823 21544 --
obs0.16823 21544 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.79 Å2
Refine analyzeLuzzati coordinate error obs: 0.156 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 0 230 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9853279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58424.48387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0081514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21205
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21657
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8761.51620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32222524
X-RAY DIFFRACTIONr_scbond_it2.2293911
X-RAY DIFFRACTIONr_scangle_it3.4924.5751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 85 -
Rwork0.209 1462 -
obs-1547 91.97 %

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