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

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Basic information

Entry
Database: PDB / ID: 2iwv
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


carbohydrate transmembrane transport / oligosaccharide transporting porin activity / 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
Outer membrane porin G
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 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 4, 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 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 G
B: OUTER MEMBRANE PROTEIN G
C: OUTER MEMBRANE PROTEIN G
D: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,101190
Polymers131,7464
Non-polymers36,355186
Water8,287460
1
A: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,70351
Polymers32,9371
Non-polymers9,76650
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,32554
Polymers32,9371
Non-polymers10,38853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,89251
Polymers32,9371
Non-polymers9,95650
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,18234
Polymers32,9371
Non-polymers6,24533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.600, 77.000, 103.900
Angle α, β, γ (deg.)79.30, 73.40, 74.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
13A
23C
33D
14A
24B
34D
15A
25B
16A
26C
17A
27D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A4 - 280
2111B4 - 280
3111C4 - 280
4111D4 - 280
1212A301 - 305
2212B301 - 305
3212C301 - 305
4212D301 - 305
1311A401 - 416
2311B401 - 416
3311C401 - 416
4311D401 - 416
1121A421 - 423
2121B421 - 423
3121C421 - 423
1131A431 - 434
2131C431 - 434
3131D431 - 434
1141A440
2141B440
3141D440
1151A452 - 454
2151B452 - 454
1161A462
2161C462
1171A471
2171D471

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
OUTER MEMBRANE PROTEIN G / OMPG


Mass: 32936.527 Da / Num. of mol.: 4 / 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: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 152 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 3.7 Å3/Da / Density % sol: 66.7 %
Crystal growpH: 7.9 / Details: 100 MM HEPES PH 7.5 30% PEG 4000 200 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.1761
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1761 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 240777 / % possible obs: 90.6 % / Observed criterion σ(I): 4.2 / Redundancy: 2.98 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.56

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→14.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 25.649 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4210 5 %RANDOM
Rwork0.224 ---
obs0.226 79984 100 %-
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: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å2-1.84 Å26.91 Å2
2---1.36 Å2-1.79 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9192 0 2476 460 12128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02111778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5042.08815500
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.57551104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00524.161596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.491151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7061560
X-RAY DIFFRACTIONr_chiral_restr0.1820.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.25201
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3410.27017
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.2174
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.19435562
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.65158714
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.35866934
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.96276786
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2543tight positional0.050.05
12B2543tight positional0.060.05
13C2543tight positional0.050.05
14D2543tight positional0.060.05
21A48tight positional0.170.05
22B48tight positional0.280.05
23C48tight positional0.250.05
31A64tight positional0.110.05
32C64tight positional0.190.05
33D64tight positional0.130.05
41A16tight positional0.040.05
42B16tight positional0.030.05
43D16tight positional0.040.05
51A48tight positional0.210.05
61A16tight positional0.090.05
71A16tight positional0.310.05
11A2543tight thermal0.10.5
12B2543tight thermal0.10.5
13C2543tight thermal0.090.5
14D2543tight thermal0.090.5
21A48tight thermal0.040.5
22B48tight thermal0.040.5
23C48tight thermal0.040.5
31A64tight thermal0.050.5
32C64tight thermal0.050.5
33D64tight thermal0.050.5
41A16tight thermal0.030.5
42B16tight thermal0.040.5
43D16tight thermal0.040.5
51A48tight thermal0.030.5
61A16tight thermal0.050.5
71A16tight thermal0.030.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 273
Rwork0.327 5198

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