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- PDB-3rpw: The crystal structure of an ABC transporter from Rhodopseudomonas... -

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Basic information

Entry
Database: PDB / ID: 3rpw
TitleThe crystal structure of an ABC transporter from Rhodopseudomonas palustris CGA009
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / outer membrane-bounded periplasmic space
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / UREA / Extracellular solute-binding protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Sep 25, 2013Group: Database references
Revision 1.4Nov 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 / pdbx_struct_special_symmetry / 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: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,52715
Polymers40,7301
Non-polymers79714
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.711, 80.711, 109.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

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Components

#1: Protein ABC transporter


Mass: 40730.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA4648 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q6N0W2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium Malonate, 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-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.65→32.5 Å / Num. all: 50234 / Num. obs: 50234 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 36.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2531 / % possible all: 100

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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: 1.65→32.5 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 2459 5.06 %random
Rwork0.1664 ---
all0.1679 48636 --
obs0.1679 48636 96.76 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.898 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4225 Å2-0 Å20 Å2
2---0.4225 Å2-0 Å2
3---0.845 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 52 227 2890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082800
X-RAY DIFFRACTIONf_angle_d1.1183798
X-RAY DIFFRACTIONf_dihedral_angle_d12.0171053
X-RAY DIFFRACTIONf_chiral_restr0.07407
X-RAY DIFFRACTIONf_plane_restr0.005487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6503-1.6820.26661300.22292360X-RAY DIFFRACTION88
1.682-1.71630.26451180.2152356X-RAY DIFFRACTION91
1.7163-1.75370.21331420.19942356X-RAY DIFFRACTION91
1.7537-1.79440.22361200.19152484X-RAY DIFFRACTION93
1.7944-1.83930.20251140.1752484X-RAY DIFFRACTION95
1.8393-1.8890.21241580.17282515X-RAY DIFFRACTION96
1.889-1.94460.23451520.17282510X-RAY DIFFRACTION97
1.9446-2.00740.20481370.16742553X-RAY DIFFRACTION98
2.0074-2.07910.21221510.16482578X-RAY DIFFRACTION98
2.0791-2.16230.19791360.16242611X-RAY DIFFRACTION99
2.1623-2.26070.20411370.16062604X-RAY DIFFRACTION99
2.2607-2.37990.18661360.16182645X-RAY DIFFRACTION99
2.3799-2.52890.2011210.17152656X-RAY DIFFRACTION99
2.5289-2.72410.21781390.1692629X-RAY DIFFRACTION99
2.7241-2.99810.19331320.17082675X-RAY DIFFRACTION100
2.9981-3.43150.16641340.15582688X-RAY DIFFRACTION100
3.4315-4.32170.17391610.14252696X-RAY DIFFRACTION100
4.3217-32.50660.18881410.17632777X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 3.0055 Å / Origin y: 50.4873 Å / Origin z: 20.4975 Å
111213212223313233
T0.0576 Å2-0.0281 Å2-0.03 Å2-0.0619 Å20.0078 Å2--0.0767 Å2
L0.1652 °2-0.008 °2-0.0549 °2-0.3662 °2-0.1296 °2--0.2248 °2
S-0.0013 Å °-0.0406 Å °0.0208 Å °0.0978 Å °-0.0485 Å °-0.1608 Å °-0.0826 Å °0.0854 Å °0.0129 Å °
Refinement TLS groupSelection details: all

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