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- PDB-1ji0: Crystal Structure Analysis of the ABC transporter from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 1ji0
TitleCrystal Structure Analysis of the ABC transporter from Thermotoga maritima
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / ATP binding protein / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


L-amino acid transport / branched-chain amino acid transmembrane transporter activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
High-affinity branched-chain amino acid transport ATP-binding protein / : / 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 ...High-affinity branched-chain amino acid transport ATP-binding protein / : / 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
ADENOSINE-5'-TRIPHOSPHATE / Branched chain amino acid ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Beasley, S. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The 2.0 A Crystal Structure of ABC Transporter from Thermotoga maritima
Authors: Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Beasley, S.
History
DepositionJun 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 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_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_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: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2512
Polymers26,7441
Non-polymers5071
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.070, 51.070, 202.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ABC transporter / BRANCHED CHAIN AMINO ACID ABC TRANSPORTER


Mass: 26743.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0M3
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Mar 6, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 2→50 Å / Num. all: 19336 / Num. obs: 19297 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 15 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 13 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / Num. unique all: 1864 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→49.52 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 591265.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1539 5.1 %RANDOM
Rwork0.242 ---
obs0.242 30374 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.76 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å20 Å2
2--4.3 Å20 Å2
3----8.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 31 182 2052
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 210 5.3 %
Rwork0.258 3773 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMATP.TOP
X-RAY DIFFRACTION3ATP.PARAM

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