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- PDB-3spx: Crystal structure of O-Acetyl Serine Sulfhydrylase from Leishmani... -

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Basic information

Entry
Database: PDB / ID: 3spx
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase from Leishmania donovani
ComponentsO-acetyl serine sulfhydrylase
KeywordsTRANSFERASE / O-Acetyl Serine Sulfhydrylase / Cysteine Synthase / Type II PLP dependent enzyme / Cysteine biocynthesis / Serine Acetyl Transferase / cytosolic
Function / homology
Function and homology information


cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / : / 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
DI(HYDROXYETHYL)ETHER / O-acetyl serine sulfhydrylase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsRaj, I. / Gourinath, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases with a range of C-terminal sequences
Authors: Raj, I. / Kumar, S. / Gourinath, S.
History
DepositionJul 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-acetyl serine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0724
Polymers35,9071
Non-polymers1653
Water3,531196
1
A: O-acetyl serine sulfhydrylase
hetero molecules

A: O-acetyl serine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1448
Polymers71,8152
Non-polymers3296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area6320 Å2
ΔGint-76 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.266, 61.974, 43.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

21A-502-

HOH

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Components

#1: Protein O-acetyl serine sulfhydrylase


Mass: 35907.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: MHOM/IM/1983/AG83 / Gene: OASS / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1C2I2, cysteine synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.24 Å3/Da / Density % sol: 45.02 % / Mosaicity: 0.418 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: KSCN, PEG 3350, Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 29852 / Num. obs: 29629 / % possible obs: 99.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.064 / Χ2: 0.997 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.835.60.38613590.752192.1
1.83-1.866.50.41513990.741196.9
1.86-1.97.30.35414440.752196.8
1.9-1.947.70.30114290.747199.5
1.94-1.9880.25914860.7481100
1.98-2.038.10.21214390.7641100
2.03-2.088.10.18815010.7831100
2.08-2.138.20.15714450.81100
2.13-2.28.20.13214790.8131100
2.2-2.278.20.11514780.8161100
2.27-2.358.20.09314770.8211100
2.35-2.448.20.08514820.7971100
2.44-2.558.20.07414890.8091100
2.55-2.698.20.06515070.841100
2.69-2.868.10.05614790.9181100
2.86-3.088.10.05315131.1511100
3.08-3.3980.05514911.741100
3.39-3.887.90.05615312.4941100
3.88-4.887.90.03515541.4951100
4.88-507.40.02416470.918199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å42.2 Å
Translation1.97 Å42.2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→42.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8612 / SU B: 2.406 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1238 / SU Rfree: 0.1207 / Cross valid method: THROUGHOUT / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1437 4.9 %RANDOM
Rwork0.176 ---
obs0.178 29499 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.07 Å2 / Biso mean: 20.7145 Å2 / Biso min: 3.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--0.25 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.79→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 9 196 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222441
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9923302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01624.48387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80215426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191513
X-RAY DIFFRACTIONr_chiral_restr0.1590.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211782
X-RAY DIFFRACTIONr_mcbond_it1.3971.51584
X-RAY DIFFRACTIONr_mcangle_it2.28522547
X-RAY DIFFRACTIONr_scbond_it3.8773857
X-RAY DIFFRACTIONr_scangle_it6.1424.5755
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 84 -
Rwork0.298 1812 -
all-1896 -
obs--87.58 %

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