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- PDB-3b1e: Crystal structure of betaC-S lyase from Streptococcus anginosus i... -

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Basic information

Entry
Database: PDB / ID: 3b1e
TitleCrystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: alpha-Aminoacrylate 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
Chem-0JO / ACETATE ION / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesStreptococcus anginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 1.2May 10, 2017Group: Non-polymer description
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 16, 2024Group: 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)182,63424
Polymers178,5974
Non-polymers4,03720
Water30,6441701
1
A: BetaC-S lyase
B: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,16911
Polymers89,2992
Non-polymers1,8709
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-15 kcal/mol
Surface area28440 Å2
MethodPISA
2
C: BetaC-S lyase
D: BetaC-S lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,46613
Polymers89,2992
Non-polymers2,16711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-24 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.204, 111.212, 217.353
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, 1721 molecules

#2: Chemical
ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13N2O7P
#3: 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
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1701 / 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: 45.91 %
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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2009
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: 1.78→72.35 Å / Num. all: 156276 / Num. obs: 156276 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 6.1
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3 / Num. unique all: 11457 / Rsym value: 0.238 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→49.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.778 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17683 7800 5 %RANDOM
Rwork0.14218 ---
all0.14391 147996 --
obs0.14391 147996 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: 9.262 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.78→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12466 0 257 1701 14424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213372
X-RAY DIFFRACTIONr_bond_other_d0.0010.028876
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9618276
X-RAY DIFFRACTIONr_angle_other_deg0.947321787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96251639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29825.148674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.763152230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721549
X-RAY DIFFRACTIONr_chiral_restr0.2460.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022610
X-RAY DIFFRACTIONr_nbd_refined0.210.22779
X-RAY DIFFRACTIONr_nbd_other0.1880.29625
X-RAY DIFFRACTIONr_nbtor_refined0.1790.26563
X-RAY DIFFRACTIONr_nbtor_other0.0830.26462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6521.57934
X-RAY DIFFRACTIONr_mcbond_other0.1811.53141
X-RAY DIFFRACTIONr_mcangle_it1.237212903
X-RAY DIFFRACTIONr_scbond_it2.12935637
X-RAY DIFFRACTIONr_scangle_it3.5024.55318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 578 -
Rwork0.156 10769 -
obs--100 %

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