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- PDB-5v2w: Crystal structure of a LuxS from salmonella typhi -

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Basic information

Entry
Database: PDB / ID: 5v2w
TitleCrystal structure of a LuxS from salmonella typhi
ComponentsS-ribosylhomocysteine lyase
KeywordsLYASE / Quroum sensing protein / LuxS / Salmonella typhi / S-ribosylhomocysteine lyase
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 speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPerumal, P. / Raina, R. / Manoj Kumar, P. / Arockisamy, A. / SundaraBaalaji, N.
Funding support India, 1items
OrganizationGrant numberCountry
ICMR2011-15260 India
CitationJournal: To Be Published
Title: Crystal structure of a LuxS from salmonella typhi
Authors: Perumal, P. / Raina, R. / Arockisamy, A. / SundaraBaalaji, N.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,0074
Polymers40,8772
Non-polymers1312
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-101 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.330, 65.453, 54.242
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 3 - 168 / Label seq-ID: 3 - 168

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
1
2

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Components

#1: Protein S-ribosylhomocysteine lyase / / AI-2 synthesis protein / Autoinducer-2 production protein LuxS


Mass: 20438.322 Da / Num. of mol.: 2 / Mutation: G21T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: luxS, STY2943, t2714 / Plasmid: pET30b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Z4D7, S-ribosylhomocysteine lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium Iodide, Bis-Trispropane, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→52 Å / Num. obs: 193762 / % possible obs: 98.5 % / Redundancy: 2.1 % / Rmerge(I) obs: 1.012 / Net I/σ(I): 2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+68 / Resolution: 2.3→52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.506 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.262 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25224 726 5.1 %RANDOM
Rwork0.18895 ---
obs0.19214 13618 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.983 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å2-0 Å2-1 Å2
2--2.68 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.3→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 2 42 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192678
X-RAY DIFFRACTIONr_bond_other_d0.0050.022520
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9553632
X-RAY DIFFRACTIONr_angle_other_deg1.03935796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6225124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4415452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0281515
X-RAY DIFFRACTIONr_chiral_restr0.080.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213062
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02592
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0263.3021359
X-RAY DIFFRACTIONr_mcbond_other2.0243.2981358
X-RAY DIFFRACTIONr_mcangle_it3.1594.9371696
X-RAY DIFFRACTIONr_mcangle_other3.1584.9411697
X-RAY DIFFRACTIONr_scbond_it2.1773.4391319
X-RAY DIFFRACTIONr_scbond_other2.1783.4431320
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3465.0891933
X-RAY DIFFRACTIONr_long_range_B_refined6.43430.63711475
X-RAY DIFFRACTIONr_long_range_B_other6.42530.59511457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9336 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 39 -
Rwork0.285 888 -
obs--87.54 %

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