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- PDB-1xt8: Crystal Structure of Cysteine-Binding Protein from Campylobacter ... -

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Basic information

Entry
Database: PDB / ID: 1xt8
TitleCrystal Structure of Cysteine-Binding Protein from Campylobacter jejuni at 2.0 A Resolution
Componentsputative amino-acid transporter periplasmic solute-binding protein
KeywordsTRANSPORT PROTEIN / ABC transport / cysteine uptake / amino-acid transporter periplasmic solute-binding protein / Campylobacter jejuni / SPINE / Structural Genomics / Structural Proteomics in Europe
Function / homology
Function and homology information


Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / : / Putative amino-acid transporter periplasmic solute-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMuller, A. / Thomas, G.H. / Horler, R. / Brannigan, J.A. / Blagova, E. / Levdikov, V.M. / Fogg, M.J. / Wilson, K.S. / Wilkinson, A.J. / Structural Proteomics in Europe (SPINE)
CitationJournal: Mol.Microbiol. / Year: 2005
Title: An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein.
Authors: Muller, A. / Thomas, G.H. / Horler, R. / Brannigan, J.A. / Blagova, E. / Levdikov, V.M. / Fogg, M.J. / Wilson, K.S. / Wilkinson, A.J.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Regarding residues -23 to 0, predicted Campylobacter jejuni leader peptide ...SEQUENCE Regarding residues -23 to 0, predicted Campylobacter jejuni leader peptide MKKILLSVLTAFVAVVLAA in the database sequence was replaced by pelB leader peptide MKYLLPTAAAGLLLLAAQPAMAMA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative amino-acid transporter periplasmic solute-binding protein
B: putative amino-acid transporter periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2345
Polymers64,9002
Non-polymers3343
Water5,837324
1
A: putative amino-acid transporter periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6923
Polymers32,4501
Non-polymers2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative amino-acid transporter periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5422
Polymers32,4501
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.863, 88.787, 72.110
Angle α, β, γ (deg.)90.00, 107.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

21A-563-

HOH

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Components

#1: Protein putative amino-acid transporter periplasmic solute-binding protein / Cysteine-Binding Protein


Mass: 32449.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: Cj0982c / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: GenBank: 15792309, UniProt: Q0P9S0*PLUS
#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, NaCl, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2004 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 30084 / Num. obs: 30084 / % possible obs: 78.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1158 / % possible all: 60.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDN

1wdn


Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.25 / SU ML: 0.136 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.222 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1518 5.1 %RANDOM
Rwork0.17738 ---
all0.18011 28444 --
obs0.18011 28444 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-2.61 Å2
2---1.35 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 20 324 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224031
X-RAY DIFFRACTIONr_bond_other_d0.0010.023632
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9665432
X-RAY DIFFRACTIONr_angle_other_deg0.78638531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93526.186194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5041510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
X-RAY DIFFRACTIONr_nbd_refined0.1980.2867
X-RAY DIFFRACTIONr_nbd_other0.1730.23682
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21967
X-RAY DIFFRACTIONr_nbtor_other0.0850.22173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.551.53220
X-RAY DIFFRACTIONr_mcbond_other0.1191.51026
X-RAY DIFFRACTIONr_mcangle_it0.69624005
X-RAY DIFFRACTIONr_scbond_it1.30431811
X-RAY DIFFRACTIONr_scangle_it1.9584.51427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 92 -
Rwork0.245 1644 -
obs-1644 100 %

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