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- PDB-2iww: Structure of the monomeric outer membrane porin OmpG in the open ... -

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Basic information

Entry
Database: PDB / ID: 2iww
TitleStructure of the monomeric outer membrane porin OmpG in the open and closed conformation
ComponentsOUTER MEMBRANE PROTEIN G
KeywordsION CHANNEL / TRANSMEMBRANE / OUTER MEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT
Function / homology
Function and homology information


oligosaccharide transporting porin activity / carbohydrate transmembrane transport / maltose transporting porin activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane porin G / Outer membrane protein G (OmpG) / monomeric porin ompg / : / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Outer membrane porin G
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsYildiz, O. / Vinothkumar, K.R. / Goswami, P. / Kuehlbrandt, W.
CitationJournal: Embo J. / Year: 2006
Title: Structure of the Monomeric Outer-Membrane Porin Ompg in the Open and Closed Conformation.
Authors: Yildiz, O. / Vinothkumar, K.R. / Goswami, P. / Kuhlbrandt, W.
History
DepositionJul 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" 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

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Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN G
B: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,33219
Polymers65,8732
Non-polymers4,45817
Water66737
1
A: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,68511
Polymers32,9371
Non-polymers2,74910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6468
Polymers32,9371
Non-polymers1,7107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.380, 71.140, 191.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA4 - 545 - 55
21ASNASNPROPROBB4 - 545 - 55
12THRTHRASNASNAA64 - 17865 - 179
22THRTHRASNASNBB64 - 17865 - 179
13GLUGLUASPASPAA187 - 215188 - 216
23GLUGLUASPASPBB187 - 215188 - 216
14ARGARGGLNGLNAA235 - 259236 - 260
24ARGARGGLNGLNBB235 - 259236 - 260
15ASPASPPHEPHEAA267 - 280268 - 281
25ASPASPPHEPHEBB267 - 280268 - 281

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Components

#1: Protein OUTER MEMBRANE PROTEIN G / OMPG


Mass: 32936.527 Da / Num. of mol.: 2 / Fragment: TRANSMEMBRANE BETA-BARREL, RESIDUES 22-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76045
#2: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.6 / Details: 100 MM NA-CITRATE PH 5.6 150 MM NACL 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 188983 / % possible obs: 92.7 % / Observed criterion σ(I): 1.75 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→19.87 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.841 / SU B: 11.749 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1342 5 %RANDOM
Rwork0.245 ---
obs0.248 25487 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---2.04 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 304 37 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225047
X-RAY DIFFRACTIONr_bond_other_d0.0060.023439
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9796837
X-RAY DIFFRACTIONr_angle_other_deg0.9563.017840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8935552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51524.161298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.38915680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5371530
X-RAY DIFFRACTIONr_chiral_restr0.0980.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021140
X-RAY DIFFRACTIONr_nbd_refined0.2360.21119
X-RAY DIFFRACTIONr_nbd_other0.2180.23529
X-RAY DIFFRACTIONr_nbtor_refined0.2120.22173
X-RAY DIFFRACTIONr_nbtor_other0.1010.22907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.89633440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.71854354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.38462838
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.45572483
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3254 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.090.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 97
Rwork0.305 1839

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