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- PDB-4xch: S-ribosylhomocysteinase from Streptococcus suis -

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Basic information

Entry
Database: PDB / ID: 4xch
TitleS-ribosylhomocysteinase from Streptococcus suis
ComponentsS-ribosylhomocysteine lyase
KeywordsLYASE / S-ribosylhomocysteinase
Function / homology
Function and homology information


S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / quorum sensing / iron ion binding
Similarity search - Function
S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) superfamily / S-Ribosylhomocysteinase (LuxS) / Metalloenzyme, LuxS/M16 peptidase-like / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWang, Y. / Mao, X. / Lu, C.
CitationJournal: To Be Published
Title: Crystal Structure of LuxS from Streptococcus suis
Authors: Wang, Y. / Mao, X. / Lu, C.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,5328
Polymers86,2704
Non-polymers2624
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-184 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.890, 86.250, 103.500
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
S-ribosylhomocysteine lyase / S-ribosylhomocysteinase / AI-2 synthesis protein / Autoinducer-2 production protein LuxS


Mass: 21567.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: HA9801 / Gene: luxS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: B2CMA5, S-ribosylhomocysteine lyase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M potassium-sodium tartrate, 0.1M sodium citrate (pH 6.5), 1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→38.2 Å / Num. obs: 50447 / % possible obs: 99.03 % / Redundancy: 13.8 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.2→38.177 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1713 5.14 %
Rwork0.1849 --
obs0.1874 33347 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 4 137 4825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084776
X-RAY DIFFRACTIONf_angle_d1.1466459
X-RAY DIFFRACTIONf_dihedral_angle_d13.7221785
X-RAY DIFFRACTIONf_chiral_restr0.077732
X-RAY DIFFRACTIONf_plane_restr0.004827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.26480.31761330.23652360X-RAY DIFFRACTION88
2.2648-2.33790.27871310.22482460X-RAY DIFFRACTION91
2.3379-2.42140.25351350.20572496X-RAY DIFFRACTION93
2.4214-2.51830.2711380.19962553X-RAY DIFFRACTION94
2.5183-2.63290.30431310.2052567X-RAY DIFFRACTION95
2.6329-2.77170.24741440.20442638X-RAY DIFFRACTION96
2.7717-2.94530.24581520.19552648X-RAY DIFFRACTION98
2.9453-3.17260.22711400.19652709X-RAY DIFFRACTION98
3.1726-3.49170.21451550.1832727X-RAY DIFFRACTION100
3.4917-3.99650.23091340.1642778X-RAY DIFFRACTION100
3.9965-5.03330.18831570.15252789X-RAY DIFFRACTION100
5.0333-38.18230.21741630.1812909X-RAY DIFFRACTION100

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