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- PDB-3sg0: The crystal structure of an extracellular ligand-binding receptor... -

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Basic information

Entry
Database: PDB / ID: 3sg0
TitleThe crystal structure of an extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2
ComponentsExtracellular ligand-binding receptor
KeywordsSIGNALING PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / ligand-binding
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOYL-FORMIC ACID / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.201 Å
AuthorsTan, K. / Mack, J.C. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2013
Title: Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.
Authors: Tan, K. / Chang, C. / Cuff, M. / Osipiuk, J. / Landorf, E. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5012
Polymers41,3511
Non-polymers1501
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.494, 70.301, 98.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. It is predicted to be a monomer.

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Components

#1: Protein Extracellular ligand-binding receptor


Mass: 41350.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: Rhodopseudomonas palustris, RPB_4630 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q2IR47
#2: Chemical ChemComp-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID


Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.6M Sodium Citrate Tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2011 / Details: Mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.2→39 Å / Num. all: 134515 / Num. obs: 134515 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 44.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / % possible all: 95.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.201→38.625 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 12.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1616 6639 5.04 %
Rwork0.1496 --
obs0.1502 131748 97.42 %
all-131748 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.194 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.436 Å20 Å20 Å2
2--0.0463 Å2-0 Å2
3----0.4823 Å2
Refinement stepCycle: LAST / Resolution: 1.201→38.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 11 527 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052927
X-RAY DIFFRACTIONf_angle_d1.113991
X-RAY DIFFRACTIONf_dihedral_angle_d12.0491151
X-RAY DIFFRACTIONf_chiral_restr0.074448
X-RAY DIFFRACTIONf_plane_restr0.006522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2009-1.21450.29261700.28613303X-RAY DIFFRACTION78
1.2145-1.22880.23772120.27083756X-RAY DIFFRACTION89
1.2288-1.24380.25561990.24163893X-RAY DIFFRACTION92
1.2438-1.25950.25632110.23023983X-RAY DIFFRACTION93
1.2595-1.27610.20782270.21464006X-RAY DIFFRACTION95
1.2761-1.29360.21182080.19634059X-RAY DIFFRACTION96
1.2936-1.31210.17372000.17784099X-RAY DIFFRACTION97
1.3121-1.33160.19242280.16794117X-RAY DIFFRACTION97
1.3316-1.35250.16262400.1534117X-RAY DIFFRACTION97
1.3525-1.37460.14462170.14914154X-RAY DIFFRACTION98
1.3746-1.39830.14842000.14344170X-RAY DIFFRACTION98
1.3983-1.42380.15832220.13934223X-RAY DIFFRACTION99
1.4238-1.45120.142270.12834181X-RAY DIFFRACTION99
1.4512-1.48080.14842250.13064170X-RAY DIFFRACTION99
1.4808-1.5130.14772230.12944262X-RAY DIFFRACTION99
1.513-1.54820.12682500.12754191X-RAY DIFFRACTION99
1.5482-1.58690.13762260.12544252X-RAY DIFFRACTION100
1.5869-1.62980.14242560.12524241X-RAY DIFFRACTION100
1.6298-1.67770.13622190.12694260X-RAY DIFFRACTION100
1.6777-1.73190.14941950.12714288X-RAY DIFFRACTION100
1.7319-1.79380.14142230.13614282X-RAY DIFFRACTION100
1.7938-1.86560.16192290.13954268X-RAY DIFFRACTION100
1.8656-1.95050.15762330.14254305X-RAY DIFFRACTION100
1.9505-2.05340.16332040.14964302X-RAY DIFFRACTION100
2.0534-2.1820.14642170.144317X-RAY DIFFRACTION100
2.182-2.35040.17582310.14144326X-RAY DIFFRACTION100
2.3504-2.58690.16612280.15194337X-RAY DIFFRACTION100
2.5869-2.96120.17712370.16384350X-RAY DIFFRACTION100
2.9612-3.73030.14542430.14644396X-RAY DIFFRACTION100
3.7303-38.64470.16232390.14874501X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 21.9011 Å / Origin y: -13.5658 Å / Origin z: -10.0911 Å
111213212223313233
T0.0688 Å2-0.0073 Å2-0.0004 Å2-0.0778 Å20.0039 Å2--0.0726 Å2
L0.4681 °2-0.1177 °2-0.2564 °2-0.4676 °20.1044 °2--0.4874 °2
S0.0307 Å °0.0303 Å °0.0208 Å °-0.0024 Å °-0.012 Å °0.009 Å °-0.0263 Å °-0.0072 Å °-0.0095 Å °
Refinement TLS groupSelection details: all

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