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- PDB-2bhs: Crystal Structure of Cysteine Synthase B -

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Basic information

Entry
Database: PDB / ID: 2bhs
TitleCrystal Structure of Cysteine Synthase 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 / cysteine synthase / L-cysteine desulfhydrase activity / cysteine biosynthetic process / cysteine synthase activity / 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 / MAD / Resolution: 2.67 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / 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 / _pdbx_entry_details.has_protein_modification / _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)131,7858
Polymers130,7964
Non-polymers9894
Water4,828268
1
A: CYSTEINE SYNTHASE B
B: CYSTEINE SYNTHASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8924
Polymers65,3982
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CYSTEINE SYNTHASE B
hetero molecules

C: CYSTEINE SYNTHASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8924
Polymers65,3982
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+3/21
MethodPQS
3
D: CYSTEINE SYNTHASE B
hetero molecules

D: CYSTEINE SYNTHASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8924
Polymers65,3982
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
MethodPQS
Unit cell
Length a, b, c (Å)195.584, 195.584, 235.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.483423, 0.873976, -0.049686), (0.874204, -0.484941, -0.024483), (-0.045493, -0.0316, -0.998465)-91.335, 171.464, 301.556
2given(0.506428, -0.862049, -0.020055), (-0.862269, -0.506413, -0.006186), (-0.004824, 0.020426, -0.99978)100.319, 284.469, 322.324
3given(0.491768, -0.870208, 0.030048), (0.87041, 0.492226, 0.009969), (-0.023465, 0.021252, 0.999499)94.227, 56.107, 9.425

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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: 32699.102 Da / Num. of mol.: 4
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.: 268 / Source method: isolated from a natural source / Formula: H2O
Compound detailsO(3)-ACETYL-L-SERINE + H(2)S = L-CYSTEINE + ACETATE.
Has protein modificationN

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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: 5 Å3/Da / Density % sol: 75 %
Crystal growpH: 5.6 / Details: pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.67→20 Å / Num. obs: 75414 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 16.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.67→19.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.318 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2263 3 %RANDOM
Rwork0.222 ---
obs0.223 73148 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.67→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8800 0 60 268 9128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0219000
X-RAY DIFFRACTIONr_bond_other_d0.0020.028363
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.97312165
X-RAY DIFFRACTIONr_angle_other_deg0.999319411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6951161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.21360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210103
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021733
X-RAY DIFFRACTIONr_nbd_refined0.220.22222
X-RAY DIFFRACTIONr_nbd_other0.2350.210489
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.25611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.55748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5229209
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54633252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7764.52956
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 163
Rwork0.326 5254

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