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- PDB-2wjr: NanC porin structure in rhombohedral crystal form. -

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Basic information

Entry
Database: PDB / ID: 2wjr
TitleNanC porin structure in rhombohedral crystal form.
ComponentsPROBABLE N-ACETYLNEURAMINIC ACID OUTER MEMBRANE CHANNEL PROTEIN NANC
KeywordsTRANSPORT PROTEIN / CELL MEMBRANE / ION TRANSPORT / TRANSMEMBRANE / PORIN / MEMBRANE / TRANSPORT / BETA-BARREL / KDGM FAMILY / MEMBRANE PROTEIN / SIALIC ACID TRANSLOCATION / MONOMERIC PORIN / SUGAR TRANSPORT / CELL OUTER MEMBRANE / CARBOHYDRATE TRANSPORT
Function / homology
Function and homology information


oligosaccharide transport / oligosaccharide transporting porin activity / sialic acid transmembrane transporter activity / sialic acid transport / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Oligogalacturonate-specific porin / Oligogalacturonate-specific porin protein (KdgM) / monomeric porin ompg / : / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-OCTANE / PHOSPHATE ION / N-acetylneuraminic acid outer membrane channel protein NanC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWirth, C. / Condemine, G. / Schirmer, T. / Peneff, C.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Nanc Crystal Structure, a Model for Outer Membrane Channels of the Acidic Sugar-Specific Kdgm Porin Family.
Authors: Wirth, C. / Condemine, G. / Boiteux, C. / Berneche, S. / Schirmer, T. / Peneff, C.M.
History
DepositionMay 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.4May 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE N-ACETYLNEURAMINIC ACID OUTER MEMBRANE CHANNEL PROTEIN NANC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4178
Polymers25,3891
Non-polymers1,0287
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.901, 74.901, 126.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PROBABLE N-ACETYLNEURAMINIC ACID OUTER MEMBRANE CHANNEL PROTEIN NANC / NANR-REGULATED CHANNEL / PORIN NANC / N-ACETYLNEURAMINIC ACID-INDUCIBLE OUTER MEMBRANE CHANNEL PROTEIN NANC


Mass: 25388.844 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-238 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PKSM717 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)OMP8/PLYS / References: UniProt: P69856
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 25 TO ALA
Nonpolymer detailsN-OCTANE (OCT): OCT ARE INCOMPLETE MODELS OF DETERGENT MOLECULES
Sequence detailsFOR CLONING PURPOSE, A1 HAS BEEN DELETED AND T2 HAS BEEN MUTATED INTO A2

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES PH 7.5, 52% PEG400, VAPOR DIFFUSION, 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 24521 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.991 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 43 TO 52 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22963 1254 5.1 %RANDOM
Rwork0.19354 ---
obs0.19527 23265 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.613 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20.88 Å20 Å2
2--1.75 Å20 Å2
3----2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 67 113 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211839
X-RAY DIFFRACTIONr_bond_other_d0.0060.021263
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9222491
X-RAY DIFFRACTIONr_angle_other_deg0.883.0052955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80123.301103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39815271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6631514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7261.51015
X-RAY DIFFRACTIONr_mcbond_other0.1661.5419
X-RAY DIFFRACTIONr_mcangle_it1.34521633
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9293824
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0374.5856
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 97 -
Rwork0.276 1753 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 3.969 Å / Origin y: -24.09 Å / Origin z: -18.562 Å
111213212223313233
T0.0208 Å20.0052 Å20.0133 Å2-0.0036 Å20.0008 Å2--0.0129 Å2
L0.5485 °20.0332 °20.0836 °2-0.6145 °2-0.1216 °2--0.5347 °2
S0.0445 Å °-0.0141 Å °0.0723 Å °0.0272 Å °-0.0139 Å °0.0179 Å °-0.0874 Å °-0.0377 Å °-0.0306 Å °

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