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- PDB-4evs: Crystal structure of ABC transporter from R. palustris - solute b... -

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Basic information

Entry
Database: PDB / ID: 4evs
TitleCrystal structure of ABC transporter from R. palustris - solute binding protein (RPA0985) in complex with 4-hydroxybenzoate
ComponentsPUTATIVE ABC TRANSPORTER SUBUNIT, SUBSTRATE-BINDING COMPONENT
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABc transporter / solute binding protein / benzoate-derivatives binding
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
Leu/Ile/Val-binding protein / : / 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
P-HYDROXYBENZOIC ACID / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMichalska, K. / Mack, J.C. / Zerbs, S. / Collart, F.R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins.
Authors: Michalska, K. / Chang, C. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Nov 20, 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: PUTATIVE ABC TRANSPORTER SUBUNIT, SUBSTRATE-BINDING COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2119
Polymers40,4001
Non-polymers8118
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.911, 61.907, 126.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE ABC TRANSPORTER SUBUNIT, SUBSTRATE-BINDING COMPONENT


Mass: 40400.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0985 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: Q6NB45
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 2 M (NH4)2SO4, 0.1 M citric acid/NaOH , pH 3.5, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 59525 / Num. obs: 59333 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 24.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2906 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→39.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.333 / SU ML: 0.04 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16416 1202 2 %RANDOM
Rwork0.13448 ---
all0.13508 59067 --
obs0.13508 59067 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--1.78 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 45 263 3089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222940
X-RAY DIFFRACTIONr_bond_other_d0.0040.021959
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9863998
X-RAY DIFFRACTIONr_angle_other_deg0.9934841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0825.327107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76815505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.297158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_mcbond_it1.6751.51871
X-RAY DIFFRACTIONr_mcbond_other0.5411.5760
X-RAY DIFFRACTIONr_mcangle_it2.55423030
X-RAY DIFFRACTIONr_scbond_it3.89231069
X-RAY DIFFRACTIONr_scangle_it5.8154.5968
X-RAY DIFFRACTIONr_rigid_bond_restr1.5334899
LS refinement shellResolution: 1.447→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 81 -
Rwork0.206 4168 -
obs-4249 98.52 %

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