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- PDB-1pc3: Crystal structure of the extracellular phosphate ABC transport re... -

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Basic information

Entry
Database: PDB / ID: 1pc3
TitleCrystal structure of the extracellular phosphate ABC transport receptor (PstS-1) and immunodominant antigen of M. tuberculosis.
ComponentsPhosphate-binding protein 1
KeywordsTRANSPORT PROTEIN / Phosphate transport receptor / immonodominant antigen / Mycobacterium tuberculosis / ion-dipole interactions / electrostatics
Function / homology
Function and homology information


phosphate ion transport / phosphate ion transmembrane transport / cellular response to phosphate starvation / cell wall / phosphate ion binding / : / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / Modulation by Mtb of host immune system / cell adhesion ...phosphate ion transport / phosphate ion transmembrane transport / cellular response to phosphate starvation / cell wall / phosphate ion binding / : / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / Modulation by Mtb of host immune system / cell adhesion / cell surface / extracellular region / plasma membrane / cytosol
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / Bacterial extracellular solute-binding protein / 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
PHOSPHATE ION / Phosphate-binding protein PstS 1 / Phosphate-binding protein PstS 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.16 Å
AuthorsVyas, N.K. / Vyas, M.N. / Quiocho, F.A.
CitationJournal: Structure / Year: 2003
Title: Crystal structure of M tuberculosis ABC phosphate transport receptor: specificity and charge compensation dominated by ion-dipole interactions.
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
History
DepositionMay 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE There are 2 alternate conformations for monomer B and its associated ligands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate-binding protein 1
B: Phosphate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8314
Polymers71,6422
Non-polymers1902
Water4,324240
1
A: Phosphate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9162
Polymers35,8211
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9162
Polymers35,8211
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.4, 72.3, 73.4
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Number of models2

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Components

#1: Protein Phosphate-binding protein 1 / PBP-1 / PstS-1 / Protein antigen B / PAB / Antigen Ag78


Mass: 35820.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: PSTS1 OR PHOS1 OR RV0934 OR MT0961 OR MTCY08D9.05C / Plasmid details: derivative of pET-9d / Plasmid: pETMPBP / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P15712, UniProt: P9WGU1*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Sep 8, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.11→18.64 Å / Num. all: 32319 / Num. obs: 32319 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 3.5 Å2 / Rmerge(I) obs: 0.0654 / Rsym value: 0.0654 / Net I/σ(I): 8
Reflection shellResolution: 2.11→2.3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 2.64 / Num. unique all: 4518 / Rsym value: 0.084 / % possible all: 79.4

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Processing

Software
NameVersionClassification
CNS1refinement
STRATEGYdata reduction
SDMSdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR
Starting model: PDB id 2ABH

2abh


Resolution: 2.16→18.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3450257.47 / Data cutoff high rms absF: 3450257.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1595 5.1 %RANDOM
Rwork0.22 ---
all0.22 31350 --
obs0.22 31350 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1561 Å2 / ksol: 0.274833 e/Å3
Displacement parametersBiso mean: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.75 Å20 Å20 Å2
2---1.7 Å20 Å2
3---6.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.16→18.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 10 240 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.272
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 2.16→2.3 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 232 4.9 %
Rwork0.265 4518 -
obs-232 79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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