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- PDB-4ymu: Crystal structure of an amino acid ABC transporter complex with a... -

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Basic information

Entry
Database: PDB / ID: 4ymu
TitleCrystal structure of an amino acid ABC transporter complex with arginines and 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
ARGININE / 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: 2.503 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 / struct_conn / struct_conn_type
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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)103,54710
Polymers102,1334
Non-polymers1,4136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-77 kcal/mol
Surface area39210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.765, 114.098, 298.636
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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.52 %
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: 2.5→49.5 Å / Num. obs: 54117 / % possible obs: 99.3 % / Redundancy: 5.9 % / Net I/σ(I): 19.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.71 / % possible all: 94.8

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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: 2.503→49.497 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 2766 5.11 %
Rwork0.224 --
obs0.2258 54117 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→49.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 88 0 7135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097242
X-RAY DIFFRACTIONf_angle_d1.2779791
X-RAY DIFFRACTIONf_dihedral_angle_d17.2632725
X-RAY DIFFRACTIONf_chiral_restr0.0861179
X-RAY DIFFRACTIONf_plane_restr0.0061212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.54620.3858810.32981685X-RAY DIFFRACTION63
2.5462-2.59250.3604970.31761923X-RAY DIFFRACTION71
2.5925-2.64230.42621110.3022121X-RAY DIFFRACTION79
2.6423-2.69630.34451320.30362356X-RAY DIFFRACTION87
2.6963-2.75490.31791450.29772516X-RAY DIFFRACTION94
2.7549-2.8190.35511300.29222601X-RAY DIFFRACTION98
2.819-2.88950.34511530.2822706X-RAY DIFFRACTION100
2.8895-2.96760.36551540.292674X-RAY DIFFRACTION100
2.9676-3.05490.37221320.27282705X-RAY DIFFRACTION100
3.0549-3.15350.30871360.25692698X-RAY DIFFRACTION100
3.1535-3.26620.32051630.24112711X-RAY DIFFRACTION100
3.2662-3.39690.30291540.23542711X-RAY DIFFRACTION100
3.3969-3.55150.24931350.22912718X-RAY DIFFRACTION100
3.5515-3.73860.271420.21052724X-RAY DIFFRACTION100
3.7386-3.97280.20971400.19872691X-RAY DIFFRACTION100
3.9728-4.27940.21411440.17552713X-RAY DIFFRACTION100
4.2794-4.70970.20731640.16682737X-RAY DIFFRACTION100
4.7097-5.39050.23051600.19082754X-RAY DIFFRACTION100
5.3905-6.78870.24671310.26222796X-RAY DIFFRACTION100
6.7887-49.50650.24021620.21642811X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -22.4012 Å / Origin y: 22.4181 Å / Origin z: 32.4543 Å
111213212223313233
T0.6053 Å20.0205 Å20.0173 Å2-0.7314 Å20.0087 Å2--0.604 Å2
L0.1201 °20.0028 °2-0.4978 °2-0.2879 °20.0324 °2--0.793 °2
S-0.0444 Å °-0.1168 Å °-0.0026 Å °0.1381 Å °0.0716 Å °0.0213 Å °-0.0046 Å °0.0798 Å °-0.0259 Å °
Refinement TLS groupSelection details: all

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