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- PDB-1joe: Crystal Structure of Autoinducer-2 Production Protein (LuxS) from... -

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Basic information

Entry
Database: PDB / ID: 1joe
TitleCrystal Structure of Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae
ComponentsAUTOINDUCER-2 PRODUCTION PROTEIN
KeywordsSIGNALING PROTEIN / LuxS / HI0491 / structural genomics / twinned crystal / Structure 2 Function Project / S2F
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 speciesHaemophilus influenzae Rd (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD(HG) / Resolution: 2.4 Å
AuthorsChen, C.C.H. / Parsons, J.F. / Lim, K. / Lehmann, C. / Tempczyk, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF AUTOINDUCER-2 PRODUCTION PROTEIN (LUXS) FROM HEAMOPHILUS INFLUENZAE--A CASE OF TWINNED CRYSTAL
Authors: Chen, C.C.H. / Parsons, J.F. / Lim, K. / Lehmann, C. / Tempczyk, A. / Eisenstein, E. / Herzberg, O.
History
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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_conn.ptnr2_label_seq_id / _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: AUTOINDUCER-2 PRODUCTION PROTEIN
B: AUTOINDUCER-2 PRODUCTION PROTEIN
C: AUTOINDUCER-2 PRODUCTION PROTEIN
D: AUTOINDUCER-2 PRODUCTION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,25712
Polymers74,1934
Non-polymers1,0648
Water2,414134
1
A: AUTOINDUCER-2 PRODUCTION PROTEIN
B: AUTOINDUCER-2 PRODUCTION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6286
Polymers37,0962
Non-polymers5324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-139 kcal/mol
Surface area12430 Å2
MethodPISA
2
C: AUTOINDUCER-2 PRODUCTION PROTEIN
D: AUTOINDUCER-2 PRODUCTION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6286
Polymers37,0962
Non-polymers5324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-143 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.530, 115.530, 51.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11C-237-

HOH

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Components

#1: Protein
AUTOINDUCER-2 PRODUCTION PROTEIN / AI-2 SYNTHESIS PROTEIN / HI0491 / LUXS


Mass: 18548.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Plasmid: PDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P44007
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Method: vapor diffusion-Hanging drop. Well Solution: PEG 4000 25%, MAGNESIUM CHLORIDE 0.2M, TRIS BUFFER 0.1M pH8.5. Drop composition: 15ul OF WELL SOLUTION, 15 ul OF PROTEIN (15mg/ml). ...Details: Method: vapor diffusion-Hanging drop. Well Solution: PEG 4000 25%, MAGNESIUM CHLORIDE 0.2M, TRIS BUFFER 0.1M pH8.5. Drop composition: 15ul OF WELL SOLUTION, 15 ul OF PROTEIN (15mg/ml). Soaking medium: PEG 4000 (27.5%), magnesium chloride 0.2M, Tris buffer 0.1M pH 8.5, Mercury Acetate 0.5mM. Soaking time: 3.5 hrs. Cryo Protectant: Lithium Formate 15%. , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 8, 2000 / Details: mirror
RadiationMonochromator: cryogenitcally-cooled SI(111)double crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 30314 / Num. obs: 30314 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.67 % / Rsym value: 0.0891 / Net I/σ(I): 15.09
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.68 / Rsym value: 0.499 / % possible all: 100

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Processing

Software
NameClassification
SHELXSphasing
MLPHAREphasing
DMmodel building
SHELXL-97refinement
X-GENdata reduction
X-GENdata scaling
DMphasing
RefinementMethod to determine structure: SAD(HG) / Resolution: 2.4→10 Å / Num. parameters: 18902 / Num. restraintsaints: 19055 / Cross valid method: free R throughout. / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: TWINNING REFINEMENT CARRIED OUT FIRST WITH CNS, THEN WITH SHELXL-97. FINAL TWINNING FRACTION: 0.349. THE PARTIALLY REFINED DE NOVO MODEL WAS VERIFIED AGAINST 1J6W WHEN THE COORDINATES WERE RELEASED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 1335 5 %random
Rwork0.2053 ---
all0.2099 26405 --
obs0.2099 26405 100 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4722.5
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 8 134 4722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.101
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.095
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 2.39→2.49 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.342 2552 -
obs--100 %

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