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- PDB-4yms: Crystal structure of an amino acid ABC transporter -

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Basic information

Entry
Database: PDB / ID: 4yms
TitleCrystal structure of an amino acid ABC transporter
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
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: 2.8 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_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_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)102,1334
Polymers102,1334
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-50 kcal/mol
Surface area39910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.096, 114.209, 302.019
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.68 %
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: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→41.54 Å / Num. obs: 37041 / % possible obs: 95.59 % / Redundancy: 6.7 % / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.14 / % possible all: 79.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHW

3dhw


Resolution: 2.8→41.536 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 1871 5.05 %
Rwork0.2257 --
obs0.2279 37041 89.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 0 0 7047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097154
X-RAY DIFFRACTIONf_angle_d1.2719661
X-RAY DIFFRACTIONf_dihedral_angle_d15.8462687
X-RAY DIFFRACTIONf_chiral_restr0.0521169
X-RAY DIFFRACTIONf_plane_restr0.0071206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.87580.436820.35361568X-RAY DIFFRACTION52
2.8758-2.96040.39141060.32011866X-RAY DIFFRACTION63
2.9604-3.05590.35031230.29322203X-RAY DIFFRACTION74
3.0559-3.16510.36451500.28492520X-RAY DIFFRACTION85
3.1651-3.29180.32411710.29252871X-RAY DIFFRACTION96
3.2918-3.44150.33971600.26762989X-RAY DIFFRACTION99
3.4415-3.62290.29711660.24112964X-RAY DIFFRACTION100
3.6229-3.84970.28491410.22263029X-RAY DIFFRACTION100
3.8497-4.14670.26061780.20793019X-RAY DIFFRACTION100
4.1467-4.56350.24291430.18613029X-RAY DIFFRACTION100
4.5635-5.22280.22861400.18193048X-RAY DIFFRACTION100
5.2228-6.57590.30831580.24823065X-RAY DIFFRACTION100
6.5759-41.54070.20591530.212999X-RAY DIFFRACTION94

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