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- PDB-1b0u: ATP-BINDING SUBUNIT OF THE HISTIDINE PERMEASE FROM SALMONELLA TYP... -

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Basic information

Entry
Database: PDB / ID: 1b0u
TitleATP-BINDING SUBUNIT OF THE HISTIDINE PERMEASE FROM SALMONELLA TYPHIMURIUM
ComponentsHISTIDINE PERMEASE
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER / HISTIDINE PERMEASE
Function / homologyABC transporter-like / AAA+ ATPase domain / ABC transporter, conserved site / P-loop containing nucleoside triphosphate hydrolase / ABC-type amino acid transport system, ATPase component, HisP-type / ABC transporter / ABC transporters family signature. / ATP-binding cassette, ABC transporter-type domain profile. / amino acid-transporting ATPase activity / ATP binding ...ABC transporter-like / AAA+ ATPase domain / ABC transporter, conserved site / P-loop containing nucleoside triphosphate hydrolase / ABC-type amino acid transport system, ATPase component, HisP-type / ABC transporter / ABC transporters family signature. / ATP-binding cassette, ABC transporter-type domain profile. / amino acid-transporting ATPase activity / ATP binding / plasma membrane / Histidine transport ATP-binding protein HisP
Function and homology information
Specimen sourceSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 1.5 Å resolution
AuthorsHung, L.-W. / Wang, I.X. / Nikaido, K. / Liu, P.-Q. / Ames, G.F.-L. / Kim, S.-H.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of the ATP-binding subunit of an ABC transporter.
Authors: Hung, L.W. / Wang, I.X. / Nikaido, K. / Liu, P.Q. / Ames, G.F. / Kim, S.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 12, 1998 / Release: Nov 17, 1999
RevisionDateData content typeGroupProviderType
1.0Nov 17, 1999Structure modelrepositoryInitial release
1.1Oct 16, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDINE PERMEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9365
Polyers29,3231
Non-polymers6144
Water5,747319
1
A: HISTIDINE PERMEASE
hetero molecules

A: HISTIDINE PERMEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,87310
Polyers58,6462
Non-polymers1,2278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_645-x+3/2,y-1/2,-z+3/41
Unit cell
γ
α
β
Length a, b, c (Å)68.809, 68.809, 148.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

#1: Protein/peptide HISTIDINE PERMEASE / ABC TRANSPORTER / HISP


Mass: 29322.834 Da / Num. of mol.: 1 / Fragment: ATP-BINDING SUBUNIT / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Genus: Salmonella / Genus (production host): Escherichia / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02915
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Formula: Cl / Chloride
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Formula: H2O / Water

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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: 2.9 / Density percent sol: 46 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: sparse matrix method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
115 mg/mlprotein11
220 %glycerol11
32 mMEDTA11
450 mMimidazol11
50.1 MHEPES11
610 mMATP11
720 %PEG600012
81.2 M12LiCl
90.1 MHEPES12
1010 mMATP12

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Data collection

DiffractionMean temperature: 1
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 5.0.2 / Synchrotron site: ALS / Beamline: 5.0.2 / Wavelength: 1.000, 0.9800, 0.97977, 0.9686
DetectorType: ADSC / Details: MIRRORS / Detector: CCD / Collection date: Jun 15, 1998
RadiationMonochromator: SI 1 1 1 / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.0001.0
20.98001.0
30.979771.0
40.96861.0
ReflectionB iso Wilson estimate: 17.1 / D resolution high: 1.5 / D resolution low: 2 / Number obs: 56098 / Rmerge I obs: 0.05 / NetI over sigmaI: 10.4 / Redundancy: 3.7 % / Percent possible obs: 97
Reflection shellRmerge I obs: 0.266 / Highest resolution: 1.5 / Lowest resolution: 1.53 / MeanI over sigI obs: 3.8 / Redundancy: 2 % / Percent possible all: 88.1
Reflection
*PLUS
D resolution high: 1.5 / D resolution low: 2 / Percent possible obs: 97 / B iso Wilson estimate: 17.1 / Redundancy: 3.7 %
Reflection shell
*PLUS
Redundancy: 2 % / MeanI over sigI obs: 3.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Data cutoff high rms absF: 47492 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 46.08 / Solvent model param ksol: 0.39
Displacement parametersB iso mean: 18.5 / Aniso B11: 1.56 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: 1.56 / Aniso B23: 0 / Aniso B33: -3.13
Least-squares processR factor R free: 0.211 / R factor R free error: 0.003 / R factor R work: 0.185 / R factor obs: 0.185 / Highest resolution: 1.5 / Lowest resolution: 2 / Number reflection R free: 5039 / Number reflection obs: 49829 / Percent reflection R free: 10.1 / Percent reflection obs: 86.3
Refine analyzeLuzzati coordinate error free: 0.18 / Luzzati coordinate error obs: 0.15 / Luzzati d res low obs: 5 / Luzzati sigma a free: 0.07 / Luzzati sigma a obs: 0.06
Refine hist #LASTHighest resolution: 1.5 / Lowest resolution: 2
Number of atoms included #LASTProtein: 2023 / Nucleic acid: 0 / Ligand: 34 / Solvent: 319 / Total: 2376
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.30
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.30
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.601.500
X-RAY DIFFRACTIONc_mcangle_it2.382.000
X-RAY DIFFRACTIONc_scbond_it8.592.000
X-RAY DIFFRACTIONc_scangle_it5.072.500
Refine LS shellHighest resolution: 1.5 / R factor R free: 0.21 / R factor R free error: 0.008 / R factor R work: 0.19 / Lowest resolution: 1.59 / Number reflection R free: 644 / Number reflection R work: 5603 / Total number of bins used: 6 / Percent reflection R free: 10.3 / Percent reflection obs: 66.2
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ATP.PARATP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Least-squares process
*PLUS
R factor all: 0.195
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.30
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.61
Refine LS shell
*PLUS
R factor R free: 0.21 / R factor R work: 0.19

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