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- PDB-4eyq: Crystal structure of solute binding protein of ABC transporter fr... -

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Basic information

Entry
Database: PDB / ID: 4eyq
TitleCrystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 in complex with caffeic acid/3-(4-HYDROXY-PHENYL)PYRUVIC ACID
ComponentsExtracellular ligand-binding receptor
KeywordsTRANSPORT PROTEIN / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / transporter / lignin degradation product
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
CAFFEIC ACID / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 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
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4Sep 25, 2013Group: Database references
Revision 1.5Nov 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

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Assembly

Deposited unit
A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5553
Polymers39,1941
Non-polymers3602
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.338, 88.338, 209.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-699-

HOH

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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 / 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-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 35893 / Num. obs: 35013 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 26.2
Reflection shellResolution: 1.95→1.97 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 3.72 / Num. unique all: 846 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data 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: 1.96→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.347 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 1741 5 %RANDOM
Rwork0.154 ---
all0.1565 34868 --
obs0.1565 34868 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.68 Å2 / Biso mean: 27.7277 Å2 / Biso min: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å2-0.97 Å20 Å2
2---1.94 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 26 202 2946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022890
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9833938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4235380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67824.554112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42815487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7731516
X-RAY DIFFRACTIONr_chiral_restr0.10.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212209
X-RAY DIFFRACTIONr_rigid_bond_restr3.74432890
X-RAY DIFFRACTIONr_sphericity_free24.332573
X-RAY DIFFRACTIONr_sphericity_bonded8.52252957
LS refinement shellResolution: 1.957→2.008 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 114 -
Rwork0.186 2120 -
all-2234 -
obs-2234 96.13 %
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)
11.65580.3345-0.192.7368-0.39680.52360.0103-0.03780.22420.15810.00380.1136-0.08010.0028-0.0140.07290.01470.03990.03430.02990.079265.194762.8545-1.3074
22.85880.75210.2361.5293-0.49880.9501-0.04350.11430.0339-0.1310.08480.11480.0634-0.0262-0.04130.05220.00490.03180.040.04310.073645.483342.9634-4.984
32.90730.0125-2.61283.47720.60382.52240.1019-0.4423-0.0920.5097-0.13530.0541-0.02380.26940.03340.1647-0.01230.0620.24180.09750.094461.261246.996115.5475
42.2080.7724-0.25311.3424-0.09810.36950.0419-0.1752-0.05450.1022-0.1041-0.1489-0.05570.06810.06220.07290.01660.01510.06310.05420.060869.731250.62283.0344
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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