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- PDB-3b1d: Crystal structure of betaC-S lyase from Streptococcus anginosus i... -

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Basic information

Entry
Database: PDB / ID: 3b1d
TitleCrystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: External 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 / Chem-PLS / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesStreptococcus anginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 1.2Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Mar 26, 2025Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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)183,15025
Polymers178,5974
Non-polymers4,55321
Water29,1121616
1
A: BetaC-S lyase
B: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,45612
Polymers89,2992
Non-polymers2,15710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-22 kcal/mol
Surface area28350 Å2
MethodPISA
2
C: BetaC-S lyase
D: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,69413
Polymers89,2992
Non-polymers2,39511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-24 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.965, 111.302, 217.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1637 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N2O8P
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1616 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 8000, 0.1M Hepes pH7.5, 0.08M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2008
RadiationMonochromator: Numerical link type 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: 1.66→36.84 Å / Num. all: 189945 / Num. obs: 189945 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.9
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.1 / Num. unique all: 13790 / Rsym value: 0.248 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→36.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.379 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1773 9529 5 %RANDOM
Rwork0.15097 ---
all0.15229 179903 --
obs0.15229 179903 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.66→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12484 0 287 1616 14387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213362
X-RAY DIFFRACTIONr_bond_other_d0.0010.028855
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9618260
X-RAY DIFFRACTIONr_angle_other_deg0.9213.00121740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84251642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54525.15668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.627152243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5961548
X-RAY DIFFRACTIONr_chiral_restr0.2420.21990
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022600
X-RAY DIFFRACTIONr_nbd_refined0.2130.22737
X-RAY DIFFRACTIONr_nbd_other0.1870.29676
X-RAY DIFFRACTIONr_nbtor_refined0.180.26609
X-RAY DIFFRACTIONr_nbtor_other0.0830.26521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.21245
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.253
X-RAY DIFFRACTIONr_mcbond_it0.621.57920
X-RAY DIFFRACTIONr_mcbond_other0.1691.53142
X-RAY DIFFRACTIONr_mcangle_it1.178212894
X-RAY DIFFRACTIONr_scbond_it2.04135639
X-RAY DIFFRACTIONr_scangle_it3.2824.55309
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 761 -
Rwork0.165 12947 -
obs--100 %

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