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- PDB-4mmp: Structure of Sialic Acid Binding Protein from Pasturella Multocida -

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Basic information

Entry
Database: PDB / ID: 4mmp
TitleStructure of Sialic Acid Binding Protein from Pasturella Multocida
ComponentsSialic Acid Binding Protein
KeywordsSUGAR BINDING PROTEIN / Sugar Transport / TRAP Transporter
Function / homologyBacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / N-acetyl-beta-neuraminic acid / :
Function and homology information
Biological speciesPasteurella multocida subsp. gallicida P1059 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsRamaswamy, S. / Thanuja, G.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site.
Authors: Gangi Setty, T. / Cho, C. / Govindappa, S. / Apicella, M.A. / Ramaswamy, S.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019.
Authors: Johnston, J.W. / Coussens, N.P. / Allen, S. / Houtman, J.C. / Turner, K.H. / Zaleski, A. / Ramaswamy, S. / Gibson, B.W. / Apicella, M.A.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic Acid Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5162
Polymers34,2071
Non-polymers3091
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.643, 77.758, 85.519
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 Sialic Acid Binding Protein / Periplasmic Sialic Acid Binding Protein / TRAP-type transport system periplasmic component


Mass: 34206.879 Da / Num. of mol.: 1 / Fragment: UNP residues 22-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida subsp. gallicida P1059 (bacteria)
Gene: SiaP, P1059_01877 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0Y3H9
#2: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drops were setup with equal volume of protein and 1.6M Sodium citrate tribasic dihydrate pH 6.5(crystallization buffer) and suspended over 100 l of crystallization buffer, VAPOR DIFFUSION, ...Details: Drops were setup with equal volume of protein and 1.6M Sodium citrate tribasic dihydrate pH 6.5(crystallization buffer) and suspended over 100 l of crystallization buffer, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→85.519 Å / Num. all: 40313 / Num. obs: 40313 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.57-1.655.30.4391.73011556480.43997.1
1.65-1.756.60.3252.23614455040.32599.7
1.75-1.886.30.2273.13287551860.22799.6
1.88-2.036.50.1644.23187448770.16499.9
2.03-2.226.20.1275.32768844590.12799.8
2.22-2.486.30.1036.32549940600.10399.8
2.48-2.866.10.0887.22223436300.08899.9
2.86-3.516.20.0778.11908530880.07799.8
3.51-4.965.90.0689.11436524250.06899.6
4.96-85.5195.70.0589.9822314360.05899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
AMoREphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B50

3b50


Resolution: 1.57→57.53 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.477 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 2016 5 %RANDOM
Rwork0.1616 ---
all0.1635 40313 --
obs0.1635 40254 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.49 Å2 / Biso mean: 21.9862 Å2 / Biso min: 10.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.57→57.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 21 193 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022477
X-RAY DIFFRACTIONr_bond_other_d0.0010.021664
X-RAY DIFFRACTIONr_angle_refined_deg2.1311.993353
X-RAY DIFFRACTIONr_angle_other_deg1.08934108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54826.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70215439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.256155
X-RAY DIFFRACTIONr_chiral_restr0.130.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 122 -
Rwork0.266 2521 -
all-2643 -
obs--94.12 %

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