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- PDB-4u00: Crystal structure of TTHA1159 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4u00
TitleCrystal structure of TTHA1159 in complex with ADP
ComponentsAmino acid ABC transporter, ATP-binding protein
KeywordsTRANSPORT PROTEIN / ABC amino acid transporter / Nucleotide binding domain / ATP binding protein
Function / homology
Function and homology information


ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC-type amino acid transport system, ATPase component, HisP-type / 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 ...ABC-type amino acid transport system, ATPase component, HisP-type / 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
ADENOSINE-5'-DIPHOSPHATE / Amino acid ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKarthiga Devi, S. / Chichili, V.P.R. / Velmurugan, D. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National University of Singapore Singapore
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural basis for the hydrolysis of ATP by a nucleotide binding subunit of an amino acid ABC transporter from Thermus thermophilus
Authors: Devi, S.K. / Chichili, V.P. / Jeyakanthan, J. / Velmurugan, D. / Sivaraman, J.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 15, 2021Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3425
Polymers27,8301
Non-polymers5114
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.107, 81.370, 49.338
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amino acid ABC transporter, ATP-binding protein


Mass: 27830.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1159 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJ55
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Bis-Tris, 25% PEG 3350, 0.2M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 13601 / % possible obs: 93.5 % / Redundancy: 3.5 % / Rsym value: 0.053 / Net I/σ(I): 17

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementResolution: 2.1→23.971 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1333 9.9 %
Rwork0.1872 --
obs0.1916 13468 93.61 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.182 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.147 Å20 Å21.9806 Å2
2--9.2619 Å2-0 Å2
3----7.1149 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 30 129 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081972
X-RAY DIFFRACTIONf_angle_d1.2642679
X-RAY DIFFRACTIONf_dihedral_angle_d18.212758
X-RAY DIFFRACTIONf_chiral_restr0.085298
X-RAY DIFFRACTIONf_plane_restr0.004342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1750.30071300.20121186X-RAY DIFFRACTION91
2.175-2.26210.26681370.18851181X-RAY DIFFRACTION92
2.2621-2.36490.30961270.1951171X-RAY DIFFRACTION91
2.3649-2.48950.27871330.19591166X-RAY DIFFRACTION90
2.4895-2.64530.28731240.20671149X-RAY DIFFRACTION89
2.6453-2.84920.25721190.21071212X-RAY DIFFRACTION93
2.8492-3.13540.25551370.19821248X-RAY DIFFRACTION96
3.1354-3.58780.24091420.18661258X-RAY DIFFRACTION97
3.5878-4.51530.16771380.16081269X-RAY DIFFRACTION98
4.5153-23.97220.19351460.18651295X-RAY DIFFRACTION98

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