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- PDB-2j1n: osmoporin OmpC -

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Basic information

Entry
Database: PDB / ID: 2j1n
Titleosmoporin OmpC
ComponentsOUTER MEMBRANE PROTEIN C
KeywordsTRANSPORT PROTEIN / BETA-BARREL / ION TRANSPORT / OSMOPORIN
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity / receptor-mediated virion attachment to host cell / DNA damage response / identical protein binding / metal ion binding
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DODECANE / Outer membrane porin C
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasle, A. / Storici, P. / Rummel, G. / Rosenbusch, J.P. / Schirmer, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Osmoporin Ompc from E. Coli at 2.0 A.
Authors: Basle, A. / Rummel, G. / Storici, P. / Rosenbusch, J.P. / Schirmer, T.
History
DepositionAug 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
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: OUTER MEMBRANE PROTEIN C
B: OUTER MEMBRANE PROTEIN C
C: OUTER MEMBRANE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02619
Polymers115,0093
Non-polymers2,01816
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-47.3 kcal/mol
Surface area42100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.779, 99.391, 74.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2032-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.890674, 0.402766, 0.210903), (0.374014, -0.385371, -0.843565), (-0.258483, 0.830222, -0.49388)-1.66905, 6.32226, 12.33651
2given(0.897283, 0.373299, -0.235649), (0.385422, -0.402167, 0.830489), (0.21525, -0.836008, -0.504735)1.76855, -6.68339, 11.84284

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Components

#1: Protein OUTER MEMBRANE PROTEIN C / OSMOPORIN OMPC / PORIN OMPC / OUTER MEMBRANE PROTEIN 1B


Mass: 38336.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BZB1107 / Plasmid: PMY150 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BZB1107 / References: UniProt: P06996
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C12H26
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFORMS PASSIVE DIFFUSION PORES WHICH ALLOW SMALL MOLECULAR WEIGHT HYDROPHILIC MATERIALS ACROSS THE ...FORMS PASSIVE DIFFUSION PORES WHICH ALLOW SMALL MOLECULAR WEIGHT HYDROPHILIC MATERIALS ACROSS THE OUTER MEMBRANE.

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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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growDetails: 25 MG/ML OMPC IN 25 MM TRIS-HCL (PH 8.0), 0.5 M NACL, 1.8 % (W/W) N-OCTYL-2- HYDROXYETHYLSULFOXIDE (C8HESO), 0.3 % (V/V) OCTYL-POLYOXYETHYLENE (OCTYL-POE) WERE EQUILIBRATED AGAINST A ...Details: 25 MG/ML OMPC IN 25 MM TRIS-HCL (PH 8.0), 0.5 M NACL, 1.8 % (W/W) N-OCTYL-2- HYDROXYETHYLSULFOXIDE (C8HESO), 0.3 % (V/V) OCTYL-POLYOXYETHYLENE (OCTYL-POE) WERE EQUILIBRATED AGAINST A RESERVOIR SOLUTION CONTAINING 25 MM TRIS-HCL (PH 8.0), 0.5 M NACL AND 28% PEG2000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.906
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906 Å / Relative weight: 1
ReflectionResolution: 1.97→35.85 Å / Num. obs: 88072 / % possible obs: 85 % / Observed criterion σ(I): -10 / Redundancy: 3.06 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.67
Reflection shellResolution: 1.97→1.98 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.55 / % possible all: 85.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OMF

2omf


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.039 / SU ML: 0.075 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN SET TO 20.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4425 5.2 %RANDOM
Rwork0.18 ---
obs0.18 85458 84.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---0.82 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 94 566 8802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218326
X-RAY DIFFRACTIONr_bond_other_d0.0010.025483
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.92611240
X-RAY DIFFRACTIONr_angle_other_deg0.788313186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03551035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18724.936468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.397151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.71539
X-RAY DIFFRACTIONr_chiral_restr0.0780.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021881
X-RAY DIFFRACTIONr_nbd_refined0.1790.21307
X-RAY DIFFRACTIONr_nbd_other0.1890.25639
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24006
X-RAY DIFFRACTIONr_nbtor_other0.0830.24518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2497
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1530.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.55213
X-RAY DIFFRACTIONr_mcbond_other0.1861.52205
X-RAY DIFFRACTIONr_mcangle_it1.26527975
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14433675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0854.53265
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 443 -
Rwork0.193 6241 -
obs--85.26 %
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)
10.1321-0.21390.01720.8811-0.16341.17630.0446-0.08820.14180.1320.02460.0451-0.28480.0497-0.0691-0.1302-0.05720.05420.1328-0.0608-0.064422.324.91719.641
20.3597-0.4276-0.06090.55670.11640.79330.0022-0.1359-0.07080.08840.01550.0730.12910.1004-0.0176-0.19160.00310.00690.1419-0.0111-0.104632.354-11.50117.575
30.0429-0.0966-0.02220.5552-0.16080.78970.02370.0891-0.0006-0.05240.02530.0465-0.00180.0716-0.049-0.2133-0.02590.00240.1423-0.0228-0.110426.4478.188-14.115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 346
2X-RAY DIFFRACTION2B1 - 346
3X-RAY DIFFRACTION3C1 - 346

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