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- PDB-5xoq: Crystal structure of O-Acetylserine Sulfhydrylase with bound Tran... -

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Basic information

Entry
Database: PDB / ID: 5xoq
TitleCrystal structure of O-Acetylserine Sulfhydrylase with bound Transcription Factor peptide inhibitor from Planctomyces limnophilus
Components
  • Cysteine synthase
  • GLY-PHE-SER-GLY-GLY-ASP-GLY-ILE
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CysK / OASS / Transcription Factor / Tf peptide / Cysteine Synthase / Planctomyces limnophilus / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cysteine synthase
Similarity search - Component
Biological speciesPlanctopirus limnophila
Planctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSingh, R.P. / Saini, N.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR India
Citation
Journal: To Be Published
Title: Crystal structure of O-Acetylserine Sulfhydrylase with bound Transcription Factor peptide inhibitor from Planctomyces limnophilus
Authors: Singh, R.P. / Saini, N.
#1: Journal: To Be Published
Title: Crystal structure of O-acetylserine sulfhydrylase with bound peptide of C-term transcription factor as inhibitor from planctomyces limnophilus
Authors: Singh, R.P. / Saini, N.
History
DepositionMay 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: GLY-PHE-SER-GLY-GLY-ASP-GLY-ILE
D: GLY-PHE-SER-GLY-GLY-ASP-GLY-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6756
Polymers67,4634
Non-polymers2122
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-32 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.041, 99.686, 125.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Cysteine synthase / / O-Acetylserine Sulfhydrylase


Mass: 33022.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290) (bacteria)
Strain: ATCC 43296 / DSM 3776 / IFAM 1008 / 290 / Gene: Plim_3256 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5STP0, cysteine synthase
#2: Protein/peptide GLY-PHE-SER-GLY-GLY-ASP-GLY-ILE


Mass: 708.720 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Planctomyces limnophilus (bacteria)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 8000, 100mM Tris pH8.5, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→25.22 Å / Num. obs: 54061 / % possible obs: 93 % / Redundancy: 1.1 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Χ2: 0.956 / Net I/av σ(I): 22.6 / Net I/σ(I): 15.6
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 4.61 / Num. unique obs: 2483 / CC1/2: 1 / Χ2: 0.7 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XA2

5xa2


Resolution: 1.87→25.216 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 2732 5.05 %
Rwork0.1623 --
obs0.1642 54056 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→25.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 14 393 5112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074809
X-RAY DIFFRACTIONf_angle_d0.8226510
X-RAY DIFFRACTIONf_dihedral_angle_d14.9862884
X-RAY DIFFRACTIONf_chiral_restr0.056736
X-RAY DIFFRACTIONf_plane_restr0.007845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8705-1.90270.2459910.19521829X-RAY DIFFRACTION67
1.9027-1.93730.21431070.18561930X-RAY DIFFRACTION72
1.9373-1.97460.21421240.16682104X-RAY DIFFRACTION78
1.9746-2.01490.24071150.16842212X-RAY DIFFRACTION81
2.0149-2.05870.21271240.16832291X-RAY DIFFRACTION85
2.0587-2.10650.21091230.16262440X-RAY DIFFRACTION89
2.1065-2.15920.23191440.16892520X-RAY DIFFRACTION94
2.1592-2.21750.21011410.17282701X-RAY DIFFRACTION98
2.2175-2.28270.21461250.17392734X-RAY DIFFRACTION99
2.2827-2.35640.22891670.1652694X-RAY DIFFRACTION100
2.3564-2.44050.21121560.16912724X-RAY DIFFRACTION100
2.4405-2.53810.2061470.16782738X-RAY DIFFRACTION100
2.5381-2.65350.19471410.16572764X-RAY DIFFRACTION100
2.6535-2.79330.21781500.1642729X-RAY DIFFRACTION100
2.7933-2.9680.19481520.17242748X-RAY DIFFRACTION100
2.968-3.19680.18781410.17162785X-RAY DIFFRACTION100
3.1968-3.51770.1821270.16722791X-RAY DIFFRACTION100
3.5177-4.02490.18911690.14332782X-RAY DIFFRACTION100
4.0249-5.06420.18051310.13912849X-RAY DIFFRACTION100
5.0642-25.21780.17761570.15992959X-RAY DIFFRACTION100

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