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- PDB-3hut: Crystal structure of a putative branched-chain amino acid ABC tra... -

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Basic information

Entry
Database: PDB / ID: 3hut
TitleCrystal structure of a putative branched-chain amino acid ABC transporter from Rhodospirillum rubrum
Componentsputative branched-chain amino acid ABC transporter
KeywordsTRANSPORT PROTEIN / Extracellular ligand-binding receptor / Receptor or Singnal protein / 11236m / PSI-2 / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / Protein Structure Initiative / Receptor
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
Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative branched-chain amino acid ABC transporter from Rhodospirillum rubrum
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative branched-chain amino acid ABC transporter


Theoretical massNumber of molelcules
Total (without water)38,6941
Polymers38,6941
Non-polymers00
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.341, 92.706, 44.432
Angle α, β, γ (deg.)90.00, 115.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative branched-chain amino acid ABC transporter / Extracellular ligand-binding receptor


Mass: 38694.480 Da / Num. of mol.: 1 / Fragment: residues 40-386
Source method: isolated from a genetically manipulated source
Details: TOP10(Invitrogen)
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Strain: ATCC 11170 or NCIB 8255 / Gene: Rru_A2873 / Plasmid: BC-pSGX3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2RQC5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM Magnesium Acetate tetrahydrate + 100mM Sodium Cacodylate pH 6.5 + 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 23896 / Num. obs: 23896 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 8.2 Å2 / Rsym value: 0.083 / Net I/σ(I): 7.4
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 2347 / Rsym value: 0.354 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.93→40.24 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 899 -RANDOM
Rwork0.183 ---
all0.198 23149 --
obs0.183 23149 96.7 %-
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-1.65 Å2
2---1.77 Å20 Å2
3---2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.93→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 0 338 2944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_degree22.4
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.289 146 -
Rwork0.22 --
obs-3471 91 %

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