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- PDB-1gaj: CRYSTAL STRUCTURE OF A NUCLEOTIDE-FREE ATP-BINDING CASSETTE FROM ... -

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Basic information

Entry
Database: PDB / ID: 1gaj
TitleCRYSTAL STRUCTURE OF A NUCLEOTIDE-FREE ATP-BINDING CASSETTE FROM AN ABC TRANSPORTER
ComponentsHIGH-AFFINITY BRANCHED CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / ABC transporter / active transport / ATPase / nucleotide-binding domain
Function / homology
Function and homology information


amino acid transport / ATP hydrolysis activity / ATP binding / plasma membrane
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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TERTIARY-BUTYL ALCOHOL / : / Probable branched-chain amino acid transport ATP-binding protein LivG
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKarpowich, N. / Yuan, Y.-R. / Dai, P.L. / Martsinkevich, O. / Millen, L. / Thomas, P.J. / Hunt, J.F.
CitationJournal: Structure / Year: 2001
Title: Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter.
Authors: Karpowich, N. / Martsinkevich, O. / Millen, L. / Yuan, Y.R. / Dai, P.L. / MacVey, K. / Thomas, P.J. / Hunt, J.F.
History
DepositionNov 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: HIGH-AFFINITY BRANCHED CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6309
Polymers29,0291
Non-polymers6028
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HIGH-AFFINITY BRANCHED CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)711,126216
Polymers696,68924
Non-polymers14,438192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
crystal symmetry operation5_456z-1,x,y+11
crystal symmetry operation6_456z-1,-x,-y+11
crystal symmetry operation7_656-z+1,-x,y+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_546y,z-1,x+11
crystal symmetry operation10_546-y,z-1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_566-y,-z+1,x+11
crystal symmetry operation13_557y,x,-z+21
crystal symmetry operation14_557-y,-x,-z+21
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_546x,z-1,-y+11
crystal symmetry operation18_546-x,z-1,y+11
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation20_566x,-z+1,y+11
crystal symmetry operation21_456z-1,y,-x+11
crystal symmetry operation22_456z-1,-y,x+11
crystal symmetry operation23_656-z+1,y,x+11
crystal symmetry operation24_656-z+1,-y,-x+11
Buried area93120 Å2
ΔGint-710 kcal/mol
Surface area222430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)137.52, 137.52, 137.52
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-700-

CL

21A-532-

HOH

31A-533-

HOH

DetailsThe biological assembly is a monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HIGH-AFFINITY BRANCHED CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN / BRAF


Mass: 29028.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL+ / References: GenBank: 1591902, UniProt: Q58663*PLUS

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Non-polymers , 5 types, 141 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES-Cl, (NH4)2SO4, PEG 400, T-butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22 mMdithiothreitol1drop
31.2 Mammonium sulfate1reservoir
44 %(v/v)t-butanol1reservoir
51.8 %(v/v)PEG4001reservoir
690 mMHEPES-Cl1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.06884 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06884 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 15956 / Num. obs: 13129 / % possible obs: 82.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 39.9 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 44.16
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 19 % / Rmerge(I) obs: 0.43 / % possible all: 69
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: X-PLOR 3.851
RfactorNum. reflection% reflectionSelection details
Rfree0.243 673 -RANDOM
Rwork0.205 ---
obs0.205 13564 82.3 %-
all-15596 --
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 31 133 2171
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.66

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