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- PDB-2i58: Crystal Structure of RafE from Streptococcus pneumoniae complexed... -

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Basic information

Entry
Database: PDB / ID: 2i58
TitleCrystal Structure of RafE from Streptococcus pneumoniae complexed with raffinose
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Complex with raffinose
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPaterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
CitationJournal: To be Published
Title: Crystal structure of apo and bound forms of RafE from Streptococcus pneumoniae
Authors: Paterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
History
DepositionAug 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0May 13, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.type / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0097
Polymers86,8942
Non-polymers1,1155
Water00
1
A: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9873
Polymers43,4471
Non-polymers5402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0224
Polymers43,4471
Non-polymers5753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.214, 119.435, 146.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 4 / Auth seq-ID: 4 - 388 / Label seq-ID: 4 - 388

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 43446.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP1897 / Plasmid: pTBL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q97NW2, UniProt: A0A0H2URJ7*PLUS
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose-(1-6)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DGlcpa1-6DGalpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25.5% PEG4000 0.085M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2006 / Details: mirrors
RadiationMonochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→49.21 Å / Num. all: 20180 / Num. obs: 20180 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.59 % / Rmerge(I) obs: 0.171 / Χ2: 1 / Net I/σ(I): 7 / Scaling rejects: 1005
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.7 / Num. measured all: 13379 / Num. unique all: 2121 / Χ2: 0.83 / % possible all: 98.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å49.21 Å
Translation2.9 Å49.21 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2 models: 2HQ0 residues 1-114 and 278-327 and 2HQ0 residues 115-277 and 328-387

2hq0

2hq0


Resolution: 2.8→46.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.885 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 971 4.8 %Conserved from 2HQ0
Rwork0.211 ---
all0.215 20129 --
obs-20129 91.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.857 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2--3.84 Å20 Å2
3----7.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 71 0 6157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226182
X-RAY DIFFRACTIONr_bond_other_d00.024089
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9538408
X-RAY DIFFRACTIONr_angle_other_deg4.60639948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1665768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20525.664286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81115974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6971516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026926
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021202
X-RAY DIFFRACTIONr_nbd_refined0.2450.21412
X-RAY DIFFRACTIONr_nbd_other0.240.24016
X-RAY DIFFRACTIONr_nbtor_refined0.20.23147
X-RAY DIFFRACTIONr_nbtor_other0.1220.22909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.23
X-RAY DIFFRACTIONr_mcbond_it1.7941.53819
X-RAY DIFFRACTIONr_mcbond_other6.1411.51564
X-RAY DIFFRACTIONr_mcangle_it3.17526143
X-RAY DIFFRACTIONr_scbond_it2.92132363
X-RAY DIFFRACTIONr_scangle_it4.694.52265
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4937 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.280.5
MEDIUM THERMAL5.982
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 78 -
Rwork0.275 1499 -
obs-1577 98.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.24820.6409-0.43622.7654-0.32941.44260.0917-0.04820.1490.1306-0.03470.0905-0.2095-0.0852-0.05710.02480.0286-0.0024-0.07440.00970.0111ChainA_domain1-3.94716.33818.743
20.87610.0969-0.27730.93540.16571.5766-0.0163-0.0101-0.05160.01910.0162-0.0377-0.00580.08920.0001-0.0692-0.0001-0.0215-0.05910.01840.02ChainA_domain29.0984.75-3.198
30.6660.4653-0.46430.84570.21072.39480.0001-0.07880.0165-0.0290.01990.0053-0.00650.0434-0.0201-0.05980.0102-0.028-0.06240.00970.0502ChainB_domain123.333-2.30435.56
41.9386-0.1619-0.5490.90660.37641.67160.08190.0508-0.24720.0399-0.10560.0540.1099-0.08730.0237-0.0234-0.012-0.0331-0.0802-0.00410.1139ChainB_domain212.785-24.87721.932
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1144 - 114
21AA278 - 327278 - 327
32AA115 - 277115 - 277
42AA328 - 388328 - 388
53BB4 - 1144 - 114
63BB278 - 327278 - 327
74BB115 - 277115 - 277
84BB328 - 388328 - 388

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