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- PDB-1sw2: Crystal structure of ProX from Archeoglobus fulgidus in complex w... -

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Basic information

Entry
Database: PDB / ID: 1sw2
TitleCrystal structure of ProX from Archeoglobus fulgidus in complex with glycine betaine
Componentsosmoprotection protein (proX)
KeywordsPROTEIN BINDING / binding-protein / compatible solutes / cation-pi interactions / non-classical hydrogen bonds
Function / homology
Function and homology information


transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / metal ion binding
Similarity search - Function
ProX-like, substrate-binding domain / Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / 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
TRIMETHYL GLYCINE / Osmoprotection protein (ProX)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchiefner, A. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for the binding of compatible solutes by ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Authors: Schiefner, A. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: osmoprotection protein (proX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2932
Polymers31,1741
Non-polymers1181
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.900, 75.900, 88.400
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-303-

HOH

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Components

#1: Protein osmoprotection protein (proX)


Mass: 31174.395 Da / Num. of mol.: 1 / Mutation: C1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: ProX / Plasmid: pASK-IBA6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(Codon plus RIL) / References: UniProt: O29280
#2: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 1500, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9774 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 15622 / Num. obs: 15622 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 40.1 Å2 / Rsym value: 0.108 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.547 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SW1

1sw1


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.617 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 771 4.9 %RANDOM
Rwork0.20091 ---
all0.20315 15622 --
obs0.20315 14849 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.106 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.04 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 8 46 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222205
X-RAY DIFFRACTIONr_bond_other_d0.0020.022028
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9832981
X-RAY DIFFRACTIONr_angle_other_deg0.85334738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615269
X-RAY DIFFRACTIONr_chiral_restr0.0920.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
X-RAY DIFFRACTIONr_nbd_refined0.2110.2470
X-RAY DIFFRACTIONr_nbd_other0.2290.22395
X-RAY DIFFRACTIONr_nbtor_other0.0870.21381
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3360.27
X-RAY DIFFRACTIONr_mcbond_it0.7781.51350
X-RAY DIFFRACTIONr_mcangle_it1.45222171
X-RAY DIFFRACTIONr_scbond_it2.0333855
X-RAY DIFFRACTIONr_scangle_it3.4484.5810
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 56
Rwork0.24 1080

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