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- PDB-2cey: Apo Structure of SiaP -

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Basic information

Entry
Database: PDB / ID: 2cey
TitleApo Structure of SiaP
ComponentsPROTEIN HI0146
KeywordsTRANSPORT / SIALIC ACID / NEU5AC2EN / ESR / PERIPLASMIC BINDING PROTEIN / TRIPARTITE ATP-INDEPENDENT PERIPLASMIC (TRAP) TRANSPORT / HAEMOPHILUS INFLUENZAE / VIRULENCE FACTOR
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sialic acid-binding periplasmic protein SiaP
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMuller, A. / Severi, E. / Mulligan, C. / Watts, A.G. / Kelly, D.J. / Wilson, K.S. / Wilkinson, A.J. / Thomas, G.H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Conservation of Structure and Mechanism in Primary and Secondary Transporters Exemplified by Siap, a Sialic Acid Binding Virulence Factor from Haemophilus Influenzae
Authors: Muller, A. / Severi, E. / Mulligan, C. / Watts, A.G. / Kelly, D.J. / Wilson, K.S. / Wilkinson, A.J. / Thomas, G.H.
History
DepositionFeb 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_symmetry
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN HI0146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4004
Polymers34,2041
Non-polymers1963
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.761, 102.508, 202.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1309-

ZN

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Components

#1: Protein PROTEIN HI0146 / SIAP


Mass: 34203.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P44542
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.25 %
Crystal growpH: 8
Details: 100 MM TRIS-HCL, PH 8.0, 20 % PEG 6000, 10 MM ZINC ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97624
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38727 / % possible obs: 77.4 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.33 / % possible all: 8.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→101.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.604 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2091 5.1 %RANDOM
Rwork0.194 ---
obs0.196 38727 75.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--1.79 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→101.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 3 295 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222428
X-RAY DIFFRACTIONr_bond_other_d0.0060.021630
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9713282
X-RAY DIFFRACTIONr_angle_other_deg1.16334014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6715307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34625.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.053154
X-RAY DIFFRACTIONr_chiral_restr0.1320.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined0.2210.2553
X-RAY DIFFRACTIONr_nbd_other0.1970.21621
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21195
X-RAY DIFFRACTIONr_nbtor_other0.0940.21154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0711.51611
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46322456
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5043982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4214.5826
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.699 8
Rwork0.497 153
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)Origin x (Å)Origin y (Å)Origin z (Å)
12.66-0.24971.00842.1604-2.00783.0797-0.0893-0.115-0.114-0.050.0171-0.11220.04590.06590.0722-0.1798-0.00590.0037-0.15260.0744-0.164311.579635.007438.756
21.20510.6853-0.24742.0872-1.61383.73060.0505-0.2742-0.4097-0.3687-0.0741-0.20680.42980.0990.0236-0.024-0.0901-0.0458-0.07120.0635-0.0758-0.027935.289115.7376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 125
2X-RAY DIFFRACTION1A213 - 254
3X-RAY DIFFRACTION2A126 - 210
4X-RAY DIFFRACTION2A256 - 306

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