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- PDB-2hq0: Structure of RafE from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 2hq0
TitleStructure of RafE from Streptococcus pneumoniae
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Periplasmic binding protein
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / 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
ACETATE ION / Sugar ABC transporter, sugar-binding protein / Sugar ABC transporter, sugar-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPaterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
CitationJournal: To be Published
Title: High resolution crystal structures of RafE from Streptococcus pneumoniae
Authors: Paterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_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: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6475
Polymers43,4471
Non-polymers2004
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.754, 77.700, 79.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sugar ABC transporter, sugar-binding protein


Mass: 43446.918 Da / Num. of mol.: 1 / Fragment: Residues 33-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: rafE / Plasmid: pTBL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q97NW2, UniProt: A0A0H2URJ7*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 2.8M (NaH2/K2H)PO4 0.1M Na acetate pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→19.19 Å / Num. all: 89237 / Num. obs: 89237 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Rmerge(I) obs: 0.043 / Χ2: 0.94 / Net I/σ(I): 11.5 / Scaling rejects: 2588
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.5 / Num. measured all: 23093 / Num. unique all: 8648 / Χ2: 1.01 / % possible all: 97

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å18.87 Å
Translation2.5 Å18.87 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HFB

2hfb


Resolution: 1.4→19.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4460 5 %RANDOM
Rwork0.161 ---
all0.163 89229 --
obs0.163 89229 99.02 %-
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: 23.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.49 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 13 442 3515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223406
X-RAY DIFFRACTIONr_bond_other_d00.022338
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9614648
X-RAY DIFFRACTIONr_angle_other_deg4.11835786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7325.844154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.535159
X-RAY DIFFRACTIONr_chiral_restr0.1520.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023872
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02653
X-RAY DIFFRACTIONr_nbd_refined0.2450.2773
X-RAY DIFFRACTIONr_nbd_other0.2340.22352
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21732
X-RAY DIFFRACTIONr_nbtor_other0.1110.21582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2311
X-RAY DIFFRACTIONr_metal_ion_refined0.2910.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.232
X-RAY DIFFRACTIONr_mcbond_it2.3241.52081
X-RAY DIFFRACTIONr_mcbond_other2.4231.5836
X-RAY DIFFRACTIONr_mcangle_it2.97223391
X-RAY DIFFRACTIONr_scbond_it4.21931325
X-RAY DIFFRACTIONr_scangle_it5.3494.51239
X-RAY DIFFRACTIONr_rigid_bond_restr2.72635744
X-RAY DIFFRACTIONr_sphericity_free15.1743445
X-RAY DIFFRACTIONr_sphericity_bonded4.03535643
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 288 -
Rwork0.246 6006 -
obs-6294 96.05 %

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