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- PDB-4o5j: Crystal structure of SabA from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4o5j
TitleCrystal structure of SabA from Helicobacter pylori
ComponentsUncharacterized protein
KeywordsCELL ADHESION / tetratricopeptide repeat / Adhesin / Carbohydrate/Sugar Binding / outer membrane protein / Helicobacter pylori
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane protein / :
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsPang, S.S. / Nguyen, S.T.S. / Whisstock, J.C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The three-dimensional structure of the extracellular adhesion domain of the sialic acid-binding adhesin SabA from Helicobacter pylori
Authors: Pang, S.S. / Nguyen, S.T.S. / Perry, A.J. / Day, C.J. / Panjikar, S. / Tiralongo, J. / Whisstock, J.C. / Kwok, T.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5154
Polymers50,2991
Non-polymers2163
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.044, 180.044, 64.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein / Sialic acid-binding adhesin SabA


Mass: 50298.727 Da / Num. of mol.: 1
Fragment: N-terminal extracellular adhesion domain, UNP residues 4-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: C694_03730, SabA / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: K4NCD9, UniProt: A0A2I8VBX7*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 6 Å3/Da / Density % sol: 79.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200mM sodium acetate, 18-20% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.9537
SYNCHROTRONAustralian Synchrotron MX220.9690, 0.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 14, 2013
ADSC QUANTUM 315r2CCDFeb 13, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.9691
30.97951
ReflectionResolution: 2.2→90.03 Å / Num. all: 60972 / Num. obs: 60966 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Biso Wilson estimate: 36.6 Å2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRpim(I) all% possible all
2.2-2.329.31.032.488250.357100
6.96-90.038.80.03351.920210.01299

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Processing

Software
NameVersionClassification
Blu-IceGUIdata collection
Auto-Rickshawphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→90.02 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 5.433 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALL
RfactorNum. reflection% reflectionSelection details
Rfree0.15939 3062 5 %RANDOM
Rwork0.1399 ---
all0.141 60970 --
obs0.1409 57908 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.126 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→90.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 14 158 3011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022900
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9413943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1425367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75226.917133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50915476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.571153
X-RAY DIFFRACTIONr_chiral_restr0.090.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212187
X-RAY DIFFRACTIONr_rigid_bond_restr13.97932900
X-RAY DIFFRACTIONr_sphericity_free63.685568
X-RAY DIFFRACTIONr_sphericity_bonded52.24952943
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 215 -
Rwork0.245 4119 -
obs--100 %

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