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- PDB-3ukj: Crystal structure of extracellular ligand-binding receptor from R... -

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Basic information

Entry
Database: PDB / ID: 3ukj
TitleCrystal structure of extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2
ComponentsExtracellular ligand-binding receptor
KeywordsTRANSPORT PROTEIN / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / transporter
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
3-(4-HYDROXY-PHENYL)PYRUVIC ACID / PRASEODYMIUM ION / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsChang, C. / Mack, J. / 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
DepositionNov 9, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 23, 2011ID: 3T23
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Oct 16, 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 / pdbx_struct_conn_angle / 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_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.pdbx_leaving_atom_flag / _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_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: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6074
Polymers39,1941
Non-polymers4133
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.685, 70.314, 104.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Extracellular ligand-binding receptor


Mass: 39194.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3575 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q2IU40
#2: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4
#3: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pr
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10 mM Nickel chloride, 0.1M Tris, 20% PEG2000 MME, 10 mM Praseodymium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 42597 / Num. obs: 42082 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 31.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.46 / Num. unique all: 2037 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.724 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 2127 5.1 %RANDOM
Rwork0.1585 ---
all0.1609 42032 --
obs0.1609 42032 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.06 Å2 / Biso mean: 18.1433 Å2 / Biso min: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--2.2 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 20 404 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222841
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9813860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3455372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20424.312109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7171517
X-RAY DIFFRACTIONr_chiral_restr0.1190.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212141
X-RAY DIFFRACTIONr_mcbond_it1.2491.51827
X-RAY DIFFRACTIONr_mcangle_it1.94722955
X-RAY DIFFRACTIONr_scbond_it3.25231014
X-RAY DIFFRACTIONr_scangle_it4.694.5905
X-RAY DIFFRACTIONr_rigid_bond_restr1.53632841
LS refinement shellResolution: 1.595→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 136 -
Rwork0.247 2657 -
all-2793 -
obs-2793 97.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03390.0013-0.00360.0478-0.00030.01560.0012-0.0003-0.00250.0001-0.0001-0.00420.00340.0019-0.00120.03450.0004-0.00010.0056-0.00040.036526.537863.7742.608
20.0484-0.01280.02260.0506-0.02030.0567-0.0006-0.0022-0.00450.00410.0019-0.00030.0025-0.0034-0.00130.0348-0.00050.00040.00550.00030.035215.650165.840128.9702
30.1695-0.03760.03420.3064-0.00230.05820.00360.00230.0021-0.0087-0.00430.008-0.002-0.00450.00070.0318-0.00010.00050.0062-0.00020.0353.641670.07055.5677
40.09280.0137-0.07450.0227-0.01820.08610.00360.00240.0053-0.00080.0007-0.0011-0.004-0.0041-0.00420.03410.0004-0.0010.0043-0.00050.036518.843175.38413.7303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 139
2X-RAY DIFFRACTION2A140 - 267
3X-RAY DIFFRACTION3A268 - 302
4X-RAY DIFFRACTION4A303 - 384

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