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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 / homology
Function and homology information


ABC-type polar-amino-acid transporter / ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC-type amino acid transport system, ATPase component, HisP-type / : / 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 ...ABC-type amino acid transport system, ATPase component, HisP-type / : / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Histidine/lysine/arginine/ornithine transport ATP-binding protein HisP
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
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.
History
DepositionNov 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Polymers29,3231
Non-polymers6144
Water5,747319
1
A: HISTIDINE PERMEASE
hetero molecules

A: HISTIDINE PERMEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,87310
Polymers58,6462
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
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-MP43212
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

#1: Protein HISTIDINE PERMEASE / ABC TRANSPORTER / HISP


Mass: 29322.834 Da / Num. of mol.: 1 / Fragment: ATP-BINDING SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / 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 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.9 Å3/Da / Density % sol: 46 %
Crystal growpH: 7 / Details: pH 7.00
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: sparse matrix method
Components of the solutions
*PLUS
IDConc.Common 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.000, 0.9800, 0.97977, 0.9686
DetectorType: ADSC / Detector: CCD / Date: Jun 15, 1998 / Details: MIRRORS
RadiationMonochromator: SI 1 1 1 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.981
30.979771
40.96861
ReflectionResolution: 1.5→20 Å / Num. obs: 56098 / % possible obs: 97 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.8 / % possible all: 88.1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / % possible obs: 97 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.1 Å2
Reflection shell
*PLUS
Redundancy: 2 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 474920 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.211 5039 10.1 %RANDOM
Rwork0.185 ---
obs0.185 49829 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.08 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--1.56 Å20 Å2
3----3.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 34 319 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_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
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_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it8.592
X-RAY DIFFRACTIONc_scangle_it5.072.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 644 10.3 %
Rwork0.19 5603 -
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
Refinement
*PLUS
Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.61
LS refinement shell
*PLUS
Rfactor Rfree: 0.21 / Rfactor Rwork: 0.19

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