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- PDB-4ymv: Crystal structure of an amino acid ABC transporter with ATPs -

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Basic information

Entry
Database: PDB / ID: 4ymv
TitleCrystal structure of an amino acid ABC transporter with ATPs
Components
  • ABC-type amino acid transport system, permease component
  • ABC-type polar amino acid transport system, ATPase component
KeywordsPROTEIN BINDING/TRANSPORT PROTEIN / ABC transporter / two binding sites / substrate specificity / membrane protein complex / PROTEIN BINDING-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


ABC-type amino acid transporter activity / amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
ABC transporter membrane protein permease protein ArtM/GltK/GlnP/TcyL/YhdX-like / ABC-type amino acid transport system, ATPase component, HisP-type / Amino acid ABC transporter, permease protein, 3-TM domain / : / MetI-like fold / MetI-like / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. ...ABC transporter membrane protein permease protein ArtM/GltK/GlnP/TcyL/YhdX-like / ABC-type amino acid transport system, ATPase component, HisP-type / Amino acid ABC transporter, permease protein, 3-TM domain / : / MetI-like fold / MetI-like / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ABC-type polar amino acid transport system, ATPase component / ABC-type amino acid transport system, permease component
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsGe, J. / Yu, J. / Yang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for substrate specificity of an amino acid ABC transporter
Authors: Yu, J. / Ge, J. / Heuveling, J. / Schneider, E. / Yang, M.
History
DepositionMar 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: ABC-type polar amino acid transport system, ATPase component
A: ABC-type polar amino acid transport system, ATPase component
D: ABC-type amino acid transport system, permease component
C: ABC-type amino acid transport system, permease component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1486
Polymers102,1334
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-53 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.527, 115.257, 301.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ABC-type polar amino acid transport system, ATPase component / NBD


Mass: 26821.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria)
Strain: MB4 / Gene: GlnQ, TTE0514 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RCC2
#2: Protein ABC-type amino acid transport system, permease component / TMD


Mass: 24245.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria)
Strain: MB4 / Gene: ArtM, TTE0513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RCC3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG4000, 0.1M NaCl, 0.1M MgCl, 0.1M Na Citrate / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→45 Å / Num. obs: 33536 / % possible obs: 98.7 % / Redundancy: 5.5 % / Net I/σ(I): 22.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.2 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHW

3dhw


Resolution: 3.003→43.508 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 1705 5.08 %
Rwork0.2102 --
obs0.2126 33536 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.003→43.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 62 0 7109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017221
X-RAY DIFFRACTIONf_angle_d1.3259766
X-RAY DIFFRACTIONf_dihedral_angle_d17.2582714
X-RAY DIFFRACTIONf_chiral_restr0.0551177
X-RAY DIFFRACTIONf_plane_restr0.0061208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0033-3.09170.47771070.35122402X-RAY DIFFRACTION91
3.0917-3.19140.33661400.30622552X-RAY DIFFRACTION96
3.1914-3.30540.28241480.27452618X-RAY DIFFRACTION98
3.3054-3.43770.29791350.24572653X-RAY DIFFRACTION99
3.4377-3.59410.34271410.23372671X-RAY DIFFRACTION100
3.5941-3.78350.25491710.20932615X-RAY DIFFRACTION100
3.7835-4.02040.23811510.19672663X-RAY DIFFRACTION100
4.0204-4.33060.19641490.16952672X-RAY DIFFRACTION100
4.3306-4.76590.2031420.15812691X-RAY DIFFRACTION100
4.7659-5.45440.2461460.18232712X-RAY DIFFRACTION100
5.4544-6.86760.30831180.24932773X-RAY DIFFRACTION100
6.8676-43.51250.24061570.20152809X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.6661 Å / Origin y: 22.7096 Å / Origin z: 32.629 Å
111213212223313233
T0.591 Å2-0.0161 Å20.0135 Å2-0.7364 Å20.0059 Å2--0.6229 Å2
L0.2065 °2-0.0256 °2-0.4592 °2-0.3229 °2-0.0432 °2--0.9155 °2
S0.0106 Å °-0.0841 Å °0.0037 Å °0.0967 Å °0.0562 Å °0.0398 Å °-0.026 Å °0.1082 Å °-0.0727 Å °
Refinement TLS groupSelection details: all

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