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- PDB-4ymx: Crystal structure of the substrate binding protein of an amino ac... -

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Basic information

Entry
Database: PDB / ID: 4ymx
TitleCrystal structure of the substrate binding protein of an amino acid ABC transporter
ComponentsABC-type amino acid transport system, periplasmic component
KeywordsTRANSPORT PROTEIN / ABC transporter / two binding sites / substrate specificity / membrane protein complex
Function / homology
Function and homology information


cell envelope / ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / ABC-type amino acid transport system, periplasmic component
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.481 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
A: ABC-type amino acid transport system, periplasmic component
B: ABC-type amino acid transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1274
Polymers57,7772
Non-polymers3502
Water13,457747
1
A: ABC-type amino acid transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0642
Polymers28,8891
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC-type amino acid transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0642
Polymers28,8891
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.026, 41.409, 75.604
Angle α, β, γ (deg.)103.73, 102.74, 90.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ABC-type amino acid transport system, periplasmic component / SBP


Mass: 28888.500 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: ArtI, TTE0512 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RCC4
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2M NaCl, 0.1M Bis-tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 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: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.48→31 Å / Num. obs: 71305 / % possible obs: 95.9 % / Redundancy: 2.2 % / Net I/σ(I): 28
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.3 / % possible all: 85.9

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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: 4I62

4i62


Resolution: 1.481→30.679 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1834 3577 5.02 %
Rwork0.1555 --
obs0.1569 71305 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.481→30.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 24 747 4263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063833
X-RAY DIFFRACTIONf_angle_d1.0035188
X-RAY DIFFRACTIONf_dihedral_angle_d12.9491504
X-RAY DIFFRACTIONf_chiral_restr0.066588
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4805-1.50.23361020.18032363X-RAY DIFFRACTION86
1.5-1.52060.21251310.16982519X-RAY DIFFRACTION94
1.5206-1.54230.20391450.15812589X-RAY DIFFRACTION95
1.5423-1.56530.19091630.15542515X-RAY DIFFRACTION94
1.5653-1.58980.21291290.16162563X-RAY DIFFRACTION94
1.5898-1.61580.19291480.1572560X-RAY DIFFRACTION95
1.6158-1.64370.22371370.16132594X-RAY DIFFRACTION95
1.6437-1.67360.19591270.15712625X-RAY DIFFRACTION95
1.6736-1.70580.19831460.15622573X-RAY DIFFRACTION95
1.7058-1.74060.19361270.1552576X-RAY DIFFRACTION95
1.7406-1.77840.19841520.14672630X-RAY DIFFRACTION96
1.7784-1.81980.19771260.15572556X-RAY DIFFRACTION96
1.8198-1.86530.1691450.15452650X-RAY DIFFRACTION96
1.8653-1.91570.20111160.15922626X-RAY DIFFRACTION96
1.9157-1.97210.2041380.15972674X-RAY DIFFRACTION96
1.9721-2.03570.17281350.15232611X-RAY DIFFRACTION96
2.0357-2.10850.17821310.15862635X-RAY DIFFRACTION97
2.1085-2.19280.1751530.14782646X-RAY DIFFRACTION97
2.1928-2.29260.16621230.15432671X-RAY DIFFRACTION97
2.2926-2.41340.20091490.15992615X-RAY DIFFRACTION98
2.4134-2.56460.20091580.16772650X-RAY DIFFRACTION98
2.5646-2.76250.19721250.16342708X-RAY DIFFRACTION98
2.7625-3.04030.15011520.15922623X-RAY DIFFRACTION98
3.0403-3.47970.18431600.15392670X-RAY DIFFRACTION98
3.4797-4.3820.14471330.13622681X-RAY DIFFRACTION98
4.382-30.68520.17741260.1552605X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 3.1257 Å / Origin y: -0.848 Å / Origin z: 0.6417 Å
111213212223313233
T0.0238 Å20.0026 Å20.005 Å2-0.0271 Å20.0015 Å2--0.0265 Å2
L0.069 °20.0497 °20.0648 °2-0.1098 °20.0592 °2--0.0927 °2
S0.0089 Å °0.0019 Å °0.0012 Å °-0.0037 Å °-0.0035 Å °0.0005 Å °0.0029 Å °0.0001 Å °-0 Å °
Refinement TLS groupSelection details: all

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