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- PDB-2heu: Atomic resolution structure of apo-form of RafE from Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 2heu
TitleAtomic resolution structure of apo-form of RafE from Streptococcus pneumoniae
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
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
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: 1.04 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
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter, sugar-binding protein
B: Sugar ABC transporter, sugar-binding protein
C: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,6859
Polymers135,4113
Non-polymers2746
Water45,7762541
1
A: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1953
Polymers45,1371
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2083
Polymers45,1371
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2823
Polymers45,1371
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.219, 129.315, 119.420
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-3427-

HOH

21B-3815-

HOH

DetailsBiological subunit is monomeric

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Components

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


Mass: 45136.852 Da / Num. of mol.: 3 / Fragment: Residues 33-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR 4 / 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2541 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.1M Tris.HCl, 0.05M CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9393 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: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.04→19.82 Å / Num. all: 543433 / Num. obs: 543433 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.12 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.97 / Net I/σ(I): 9.8 / Scaling rejects: 16905
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. measured all: 162181 / Num. unique all: 52441 / Χ2: 1.05 / % possible all: 94.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.82 Å
Translation3 Å19.82 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→19.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.157 27325 5 %Extended from low resolution model
Rwork0.13 ---
all0.131 543423 --
obs0.131 516098 97.58 %-
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: 11.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.39 Å2
2--0.08 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.04→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10310 0 13 2552 12875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02210647
X-RAY DIFFRACTIONr_bond_other_d00.027259
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.95514555
X-RAY DIFFRACTIONr_angle_other_deg4.247317965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02451406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97126.081495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.037151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.091526
X-RAY DIFFRACTIONr_chiral_restr0.140.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212335
X-RAY DIFFRACTIONr_gen_planes_other0.0150.022059
X-RAY DIFFRACTIONr_nbd_refined0.2670.22683
X-RAY DIFFRACTIONr_nbd_other0.2490.27621
X-RAY DIFFRACTIONr_nbtor_refined0.1910.25519
X-RAY DIFFRACTIONr_nbtor_other0.1140.25085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.21772
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.2220
X-RAY DIFFRACTIONr_mcbond_it2.2631.56526
X-RAY DIFFRACTIONr_mcbond_other4.0411.52617
X-RAY DIFFRACTIONr_mcangle_it3.057210680
X-RAY DIFFRACTIONr_scbond_it4.23934121
X-RAY DIFFRACTIONr_scangle_it5.7324.53857
X-RAY DIFFRACTIONr_rigid_bond_restr3.097317906
X-RAY DIFFRACTIONr_sphericity_free15.10332557
X-RAY DIFFRACTIONr_sphericity_bonded5.939317577
LS refinement shellResolution: 1.04→1.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 1889 -
Rwork0.226 36805 -
obs-38694 94.17 %

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