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- PDB-2bht: Crystal structure of O-acetylserine sulfhydrylase B -

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Basic information

Entry
Database: PDB / ID: 2bht
TitleCrystal structure of O-acetylserine sulfhydrylase B
ComponentsCYSTEINE SYNTHASE B
KeywordsTRANSFERASE / CYSTEINE BIOSYNTHESIS / PLP-DEPENDENT ENZYME / PYRIDOXAL-5'-PHOSPHATE / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


cysteine biosynthetic process via S-sulfo-L-cysteine / L-cysteine catabolic process to pyruvate / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / iron-sulfur cluster assembly / pyridoxal phosphate binding / protein homodimerization activity / 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 speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsClaus, M.T. / Zocher, G.E. / Maier, T.H.P. / Schulz, G.E.
CitationJournal: Biochemistry / Year: 2005
Title: Structure of the O-Acetylserine Sulfhydrylase Isoenzyme Cysm from Escherichia Coli
Authors: Claus, M.T. / Zocher, G.E. / Maier, T.H.P. / Schulz, G.E.
History
DepositionJan 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYSTEINE SYNTHASE B
B: CYSTEINE SYNTHASE B
C: CYSTEINE SYNTHASE B
D: CYSTEINE SYNTHASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6498
Polymers130,6604
Non-polymers9894
Water4,017223
1
A: CYSTEINE SYNTHASE B
B: CYSTEINE SYNTHASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8244
Polymers65,3302
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-15.5 kcal/mol
Surface area22390 Å2
MethodPISA
2
C: CYSTEINE SYNTHASE B
D: CYSTEINE SYNTHASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8244
Polymers65,3302
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-13.3 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.940, 149.940, 194.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.358025, 0.886114, -0.294314), (0.892218, 0.231752, -0.387606), (-0.275255, -0.401365, -0.87358)27.388, 72.63, 289.012
2given(0.008029, -0.99995, -0.005918), (-0.999943, -0.00807, 0.007026), (-0.007073, 0.005861, -0.999958)150.057, 149.708, 245.237
3given(-0.889894, 0.353603, 0.28819), (-0.227184, -0.891386, 0.392197), (0.39557, 0.283542, 0.873572)35.437, 145.021, -27.027

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Components

#1: Protein
CYSTEINE SYNTHASE B / O-ACETYLSERINE SULFHYDRYLASE B / O-ACETYLSERINE (THIOL)-LYASE B / CSASE B / O-ACETYLSERINE SULFHYDRYLASE B


Mass: 32665.105 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINK BETWEEN A41 AND PLP320 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PASK-IBA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16703, cysteine synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 57 TO ARG ENGINEERED RESIDUE IN CHAIN A, TYR 148 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, GLU 57 TO ARG ENGINEERED RESIDUE IN CHAIN A, TYR 148 TO LYS ENGINEERED RESIDUE IN CHAIN A, ARG 184 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLU 57 TO ARG ENGINEERED RESIDUE IN CHAIN B, TYR 148 TO LYS ENGINEERED RESIDUE IN CHAIN B, ARG 184 TO GLU ENGINEERED RESIDUE IN CHAIN C, GLU 57 TO ARG ENGINEERED RESIDUE IN CHAIN C, TYR 148 TO LYS ENGINEERED RESIDUE IN CHAIN C, ARG 184 TO GLU ENGINEERED RESIDUE IN CHAIN D, GLU 57 TO ARG ENGINEERED RESIDUE IN CHAIN D, TYR 148 TO LYS ENGINEERED RESIDUE IN CHAIN D, ARG 184 TO GLU

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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: 4.2 Å3/Da / Density % sol: 70 %
Crystal growpH: 7.6 / Details: pH 7.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.82
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 123872 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHS

2bhs


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4937 3 %RANDOM
obs0.225 -99.8 %-
all-123872 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8695 0 60 223 8978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d1.1
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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