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- PDB-2jc3: Structure of O-Acetylserine Sulfhydrylase B from Salmonella Typhi... -

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Basic information

Entry
Database: PDB / ID: 2jc3
TitleStructure of O-Acetylserine Sulfhydrylase B from Salmonella Typhimurium
ComponentsO-ACETYLSERINE SULFHYDRYLASE B
KeywordsTRANSFERASE / SULFHYDRYLASE / PYRIDOXAL PHOSPHATE / VITAMIN B6 DEPENDENT ENZYME / CYSTEINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS
Function / homology
Function and homology information


cysteine synthase / cysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysM / 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 CysM / 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
PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase B
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChattopadhyay, A. / Rabeh, W.M. / Speroni, F. / Meier, M. / Ivaninskii, S. / Mozzarelli, A. / Burkhard, P. / Cook, P.F.
CitationJournal: Biochemistry / Year: 2007
Title: Structure, Mechanism, and Conformational Dynamics of O-Acetylserine Sulfhydrylase from Salmonella Typhimurium: Comparison of a and B Isozymes.
Authors: Chattopadhyay, A. / Meier, M. / Ivaninskii, S. / Burkhard, P. / Speroni, F. / Campanini, B. / Bettati, S. / Mozzarelli, A. / Rabeh, W.M. / Li, L. / Cook, P.F.
History
DepositionDec 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-ACETYLSERINE SULFHYDRYLASE B
B: O-ACETYLSERINE SULFHYDRYLASE B
C: O-ACETYLSERINE SULFHYDRYLASE B
D: O-ACETYLSERINE SULFHYDRYLASE B
E: O-ACETYLSERINE SULFHYDRYLASE B
F: O-ACETYLSERINE SULFHYDRYLASE B
G: O-ACETYLSERINE SULFHYDRYLASE B
H: O-ACETYLSERINE SULFHYDRYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,41816
Polymers261,4418
Non-polymers1,9778
Water11,313628
1
A: O-ACETYLSERINE SULFHYDRYLASE B
B: O-ACETYLSERINE SULFHYDRYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8544
Polymers65,3602
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: O-ACETYLSERINE SULFHYDRYLASE B
D: O-ACETYLSERINE SULFHYDRYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8544
Polymers65,3602
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: O-ACETYLSERINE SULFHYDRYLASE B
F: O-ACETYLSERINE SULFHYDRYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8544
Polymers65,3602
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: O-ACETYLSERINE SULFHYDRYLASE B
H: O-ACETYLSERINE SULFHYDRYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8544
Polymers65,3602
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.052, 106.948, 112.107
Angle α, β, γ (deg.)95.59, 90.06, 117.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.94186, 0.31532, 0.11608), (0.31335, 0.69956, 0.6422), (0.1213, 0.64124, -0.75769)-0.39305, -6.0E-5, 0.01913
2given(0.39743, -0.87351, -0.2811), (-0.8539, -0.46422, 0.23529), (-0.33602, 0.14652, -0.93039)41.93711, 73.1962, 65.02917
3given(-0.67393, -0.6814, -0.28551), (0.69236, -0.44765, -0.5659), (0.25779, -0.57906, 0.77346)41.75765, 73.65274, 65.00638
4given(0.41956, -0.85835, -0.2953), (0.836, 0.49214, -0.2427), (0.35365, -0.14505, 0.92406)40.60934, 18.14099, 82.92822
5given(-0.70015, -0.66591, -0.2576), (-0.65962, 0.46517, 0.59035), (-0.27329, 0.58325, -0.76494)40.40276, 17.72482, 82.87394
6given(0.99995, -0.00974, -0.00199), (-0.0097, -0.99981, 0.01717), (-0.00215, -0.01715, -0.99985)51.62861, 9.85065, 36.2871
7given(-0.9458, 0.30612, 0.1084), (-0.29921, -0.6917, -0.65729), (-0.12623, -0.6541, 0.7458)51.23034, 9.84588, 36.21343

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Components

#1: Protein
O-ACETYLSERINE SULFHYDRYLASE B / O-ACETYLSERINE / THIOL-LYASE B / CSASE B


Mass: 32680.082 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: PLP (PYRIDOXAL 5'-PHOSPHATE) COVALENTLY LINKED TO K41
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: WR-OASSB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29848
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 4.17 Å3/Da / Density % sol: 70 %
Crystal growpH: 6
Details: PRECIPITANT: 1M NA-K TARTARATE BUFFER: 0.1 M MES, PH 6.0 PROTEIN CONCENTRATION: 23 MG/ML DROP VOLUME: 4 UL (TOTAL)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9511
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2004 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LIQUID N2 COOLED FIXED- EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9511 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 179465 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 1.5 / % possible all: 91.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAS

1oas


Resolution: 2.3→19.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 584917.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: RESIDUES 294-302 DISORDERED IN ALL CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 8993 5 %RANDOM
Rwork0.213 ---
obs0.213 179453 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.004 Å2 / ksol: 0.37111 e/Å3
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å28.66 Å21.69 Å2
2--8.01 Å22.77 Å2
3----9.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17696 0 120 628 18444
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.041.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it3.432
X-RAY DIFFRACTIONc_scangle_it4.632.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 1403 4.9 %
Rwork0.368 27022 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.PLPTOPH.PLP

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