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- PDB-4rvc: Structure of ATP binding subunit of ABC transporter -

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Basic information

Entry
Database: PDB / ID: 4rvc
TitleStructure of ATP binding subunit of ABC transporter
ComponentsABC transporter ATP-binding protein
KeywordsTRANSPORT PROTEIN / Motif C / ATP bindig
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsManjula, M. / Pampa, K.J. / Lokanath, N.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus.
Authors: Manjula, M. / Pampa, K.J. / Kumar, S.M. / Mukherjee, S. / Kunishima, N. / Rangappa, K.S. / Lokanath, N.K.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ABC transporter ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)27,5551
Polymers27,5551
Non-polymers00
Water3,711206
1
A: ABC transporter ATP-binding protein

A: ABC transporter ATP-binding protein

A: ABC transporter ATP-binding protein

A: ABC transporter ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)110,2204
Polymers110,2204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area7690 Å2
ΔGint-53 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.941, 78.637, 112.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ABC transporter ATP-binding protein


Mass: 27554.910 Da / Num. of mol.: 1 / Fragment: UNP residues 13-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: GBlys / Gene: GBL_2030 / Production host: Escherichia coli (E. coli) / References: UniProt: U2YAF6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1 M MES-NaOH, 27.5% PEG 4000, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 14, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 24183 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.77 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1169 -RANDOM
Rwork0.216 ---
obs0.25 24182 99.9 %-
all-24183 --
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 0 206 2105
Refine LS restraintsType: c_angle_d / Dev ideal: 0.02

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