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- PDB-3a2s: Crystal Structure of outer membrane protein PorB from Neisseria m... -

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Basic information

Entry
Database: PDB / ID: 3a2s
TitleCrystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with sucrose
ComponentsOuter membrane protein II
KeywordsMEMBRANE PROTEIN / Beta barrel / outer membrane protein / porin / Neisseria meningitidis / Cell membrane / Cell outer membrane / Ion transport / Membrane / Transmembrane / TRANSPORT PROTEIN / IMMUNE SYSTEM
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
sucrose / Major outer membrane protein P.IB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTanabe, M. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
Authors: Tanabe, M. / Nimigean, C.M. / Iverson, T.M.
History
DepositionJun 4, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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
X: Outer membrane protein II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7513
Polymers38,1791
Non-polymers5722
Water3,027168
1
X: Outer membrane protein II
hetero molecules

X: Outer membrane protein II
hetero molecules

X: Outer membrane protein II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2539
Polymers114,5383
Non-polymers1,7156
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11310 Å2
ΔGint-35 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.773, 82.773, 106.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11X-466-

HOH

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Components

#1: Protein Outer membrane protein II


Mass: 38179.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: porB / Plasmid: pET21bPorB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5RT80*PLUS
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES, 50mM CsCl, 28-32% Jeffamine M-600, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.978 Å
DetectorDate: Jan 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20889 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rsym value: 0.067 / Net I/σ(I): 22
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1446 / Rsym value: 0.364 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A2R

3a2r
PDB Unreleased entry


Resolution: 2.2→41.38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.552 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25575 975 4.7 %RANDOM
Rwork0.20914 ---
obs0.21148 19952 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.705 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 35 168 2796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222677
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9383608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53824.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71615431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7761514
X-RAY DIFFRACTIONr_chiral_restr0.090.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022047
X-RAY DIFFRACTIONr_nbd_refined0.1960.21098
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.28
X-RAY DIFFRACTIONr_mcbond_it0.6971.51721
X-RAY DIFFRACTIONr_mcangle_it1.2122636
X-RAY DIFFRACTIONr_scbond_it1.59431111
X-RAY DIFFRACTIONr_scangle_it2.4054.5972
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 64 -
Rwork0.213 1429 -
obs--96.57 %

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