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- PDB-3b1c: Crystal structure of betaC-S lyase from Streptococcus anginosus: ... -

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Basic information

Entry
Database: PDB / ID: 3b1c
TitleCrystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form
ComponentsBetaC-S lyase
KeywordsLYASE
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding / lyase activity
Similarity search - Function
: / Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesStreptococcus anginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKezuka, Y. / Yoshida, Y. / Nonaka, T.
Citation
Journal: Proteins / Year: 2012
Title: Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Authors: Kezuka, Y. / Yoshida, Y. / Nonaka, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary X-ray analysis of betaC-S lyases from two oral Streptococci
Authors: Kezuka, Y. / Yoshida, Y. / Nonaka, T.
#2: Journal: Oral Microbiol.Immunol. / Year: 2008
Title: Molecular and enzymatic characterization of betaC-S lyase in Streptococcus constellatus
Authors: Yoshida, Y. / Ito, S. / Sasaki, T. / Kishi, M. / Kurota, M. / Suwabe, A. / Kunimatsu, K. / Kato, H.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Differences in the betaC-S lyase activities of viridans group streptococci
Authors: Yoshida, Y. / Negishi, M. / Amano, A. / Oho, T. / Nakano, Y.
#4: Journal: Microbiology / Year: 2002
Title: lcd from Streptococcus anginosus encodes a C-S lyase with alpha,beta-elimination activity that degrades L-cysteine
Authors: Yoshida, Y. / Nakano, Y. / Amano, A. / Yoshimura, M. / Fukamachi, H. / Oho, T. / Koga, T.
History
DepositionJun 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: BetaC-S lyase
B: BetaC-S lyase
C: BetaC-S lyase
D: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,45128
Polymers178,5974
Non-polymers2,85424
Water26,4101466
1
A: BetaC-S lyase
B: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,72614
Polymers89,2992
Non-polymers1,42712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-85 kcal/mol
Surface area27220 Å2
MethodPISA
2
C: BetaC-S lyase
D: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,72614
Polymers89,2992
Non-polymers1,42712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-89 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.970, 111.140, 216.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
BetaC-S lyase


Mass: 44649.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus anginosus (bacteria) / Strain: IMU102 / Gene: lcd / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6BMJ3, cystathionine beta-lyase
#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1466 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M Ammonium sulfate, 0.1M Hepes pH7.5, 0.1M Sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 26, 2008
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→108.47 Å / Num. all: 122200 / Num. obs: 122200 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Rsym value: 0.061
Reflection shellResolution: 1.93→1.97 Å / Rmerge(I) obs: 0.23 / Num. unique all: 7249 / Rsym value: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→108.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.679 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18772 6130 5 %RANDOM
Rwork0.14718 ---
all0.14923 115973 --
obs0.14923 115973 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.93→108.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12475 0 174 1466 14115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213229
X-RAY DIFFRACTIONr_bond_other_d0.0060.028747
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.95518051
X-RAY DIFFRACTIONr_angle_other_deg0.958321479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29351625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40625.165668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.148152225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1781547
X-RAY DIFFRACTIONr_chiral_restr0.0920.21975
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022587
X-RAY DIFFRACTIONr_nbd_refined0.2060.22649
X-RAY DIFFRACTIONr_nbd_other0.1930.29365
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26376
X-RAY DIFFRACTIONr_nbtor_other0.0850.26239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.21221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2691.510285
X-RAY DIFFRACTIONr_mcbond_other0.2021.53126
X-RAY DIFFRACTIONr_mcangle_it1.175212801
X-RAY DIFFRACTIONr_scbond_it2.3436336
X-RAY DIFFRACTIONr_scangle_it3.1544.55206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 460 -
Rwork0.149 8477 -
obs--99.99 %

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