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- PDB-4ymw: Crystal structure of an amino acid ABC transporter with histidines -

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Basic information

Entry
Database: PDB / ID: 4ymw
TitleCrystal structure of an amino acid ABC transporter with histidines
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
HISTIDINE / 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: 2.804 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4466
Polymers102,1334
Non-polymers3122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-51 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.247, 115.264, 301.185
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-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG4000, 0.1M NaCl, 0.1M MgCl, 0.1M Na Citrate

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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: 2.8→35 Å / Num. obs: 38389 / % possible obs: 92.9 % / Redundancy: 4.3 % / Net I/σ(I): 22
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 74.4

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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: 2.804→34.722 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2785 1941 5.06 %
Rwork0.2242 --
obs0.2269 38389 92.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.804→34.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 20 0 7067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017174
X-RAY DIFFRACTIONf_angle_d1.489685
X-RAY DIFFRACTIONf_dihedral_angle_d15.282691
X-RAY DIFFRACTIONf_chiral_restr0.0591171
X-RAY DIFFRACTIONf_plane_restr0.0071208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8045-2.87460.39891040.33331979X-RAY DIFFRACTION71
2.8746-2.95230.43281260.32012118X-RAY DIFFRACTION78
2.9523-3.03910.39911250.3192328X-RAY DIFFRACTION84
3.0391-3.13710.37581310.30632538X-RAY DIFFRACTION91
3.1371-3.24920.31021380.26982636X-RAY DIFFRACTION95
3.2492-3.37920.3271500.24872682X-RAY DIFFRACTION96
3.3792-3.53280.30061580.23562744X-RAY DIFFRACTION99
3.5328-3.71890.30681410.22432810X-RAY DIFFRACTION100
3.7189-3.95160.2771450.22022790X-RAY DIFFRACTION100
3.9516-4.25620.26321290.19262786X-RAY DIFFRACTION99
4.2562-4.68360.23181320.17442825X-RAY DIFFRACTION99
4.6836-5.35920.22521610.18762824X-RAY DIFFRACTION99
5.3592-6.74390.31311690.25512813X-RAY DIFFRACTION100
6.7439-34.72440.22891320.21152575X-RAY DIFFRACTION86

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