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- PDB-5bnd: Crystal structure of the C-terminal domain of TagH -

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Basic information

Entry
Database: PDB / ID: 5bnd
TitleCrystal structure of the C-terminal domain of TagH
ComponentsABC transporter, ATP-binding protein
KeywordsTRANSPORT PROTEIN / transporter
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / : / Teichoic acid transporter subunit TagH C-terminal domain / Teichoic acid transporter subunit TagH, SH3-like domain / : / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsChen, S.C. / Chen, Y.
CitationJournal: Proteins / Year: 2016
Title: SH3-Like Motif-Containing C-terminal Domain of Staphylococcal Teichoic Acid Transporter Suggests Possible Function.
Authors: Ko, T.P. / Tseng, S.T. / Lai, S.J. / Chen, S.C. / Guan, H.H. / Yang, C.S. / Chen, C.J. / Chen, Y.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, ATP-binding protein
B: ABC transporter, ATP-binding protein
C: ABC transporter, ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)62,9493
Polymers62,9493
Non-polymers00
Water2,594144
1
A: ABC transporter, ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)20,9831
Polymers20,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)20,9831
Polymers20,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ABC transporter, ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)20,9831
Polymers20,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.576, 124.749, 56.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ABC transporter, ATP-binding protein


Mass: 20983.000 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 327-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 35984 / RP62A) (bacteria)
Strain: ATCC 35984 / RP62A / Gene: SERP1409 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5HN63
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 12 % PEG 3350, 0.1 M malic acid (pH 7.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→33.413 Å / Num. obs: 18143 / % possible obs: 99.2 % / Redundancy: 5 % / Net I/σ(I): 3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→33.413 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1028 5.1 %
Rwork0.2058 --
obs0.2085 18143 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→33.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 0 144 4584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014548
X-RAY DIFFRACTIONf_angle_d1.326132
X-RAY DIFFRACTIONf_dihedral_angle_d15.0591722
X-RAY DIFFRACTIONf_chiral_restr0.056660
X-RAY DIFFRACTIONf_plane_restr0.007762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6801-2.82140.33851300.29742107X-RAY DIFFRACTION75
2.8214-2.9980.30541400.27482604X-RAY DIFFRACTION93
2.998-3.22930.30281510.24262814X-RAY DIFFRACTION99
3.2293-3.5540.29441540.22022860X-RAY DIFFRACTION100
3.554-4.06750.24631570.2022867X-RAY DIFFRACTION100
4.0675-5.12160.20521530.15942884X-RAY DIFFRACTION99
5.1216-33.41580.23491430.1862991X-RAY DIFFRACTION98

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