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- PDB-3pox: Crystal Structure of E.coli OmpF porin in lipidic cubic phase: sp... -

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Basic information

Entry
Database: PDB / ID: 3pox
TitleCrystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1
ComponentsOmpF protein
KeywordsMEMBRANE PROTEIN / beta barrel / solute transport / pore
Function / homology
Function and homology information


colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity / lipid binding / membrane / identical protein binding
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / THIOCYANATE ION / : / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia Coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsEfremov, R.G. / Sazanov, L.A.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structure of Escherichia coli OmpF porin from lipidic mesophase.
Authors: Efremov, R.G. / Sazanov, L.A.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_asym_id / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpF protein
B: OmpF protein
C: OmpF protein
D: OmpF protein
E: OmpF protein
F: OmpF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,191120
Polymers222,6866
Non-polymers32,506114
Water27,4191522
1
A: OmpF protein
B: OmpF protein
C: OmpF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,31278
Polymers111,3433
Non-polymers22,96975
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-55 kcal/mol
Surface area40740 Å2
MethodPISA
2
D: OmpF protein
E: OmpF protein
F: OmpF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,88042
Polymers111,3433
Non-polymers9,53739
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-54 kcal/mol
Surface area40900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.574, 86.017, 116.558
Angle α, β, γ (deg.)83.280, 78.460, 89.890
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
OmpF protein / Outer membrane protein F


Mass: 37114.250 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 23-362 / Source method: isolated from a natural source / Source: (natural) Escherichia Coli (E. coli) / Strain: BL21List of strains of Escherichia coli / References: UniProt: C5W2U9, UniProt: P02931*PLUS
#2: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 88 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1522 / 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: 3.49 Å3/Da / Density % sol: 64.71 % / Mosaicity: 0.55 °
Crystal growTemperature: 296 K / pH: 6.5
Details: 0.1M MES, 1.9M potassium thiocyanate, pH 6.5, lipidic sponge phase, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 22, 2009 / Details: mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→19.998 Å / Num. all: 196203 / Num. obs: 196203 / % possible obs: 97.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.141 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.112.10.7150.5261.160204284450.4820.7150.5261.796.4
2.11-2.242.10.520.3831.757607269280.3480.520.3832.396.8
2.24-2.392.20.4360.3231.455084254430.2910.4360.323397
2.39-2.582.20.3110.2322.751897236990.2060.3110.2323.997.4
2.58-2.832.20.2310.1733.148383218820.1520.2310.1735.397.6
2.83-3.162.20.1720.133.444011198680.1120.1720.137.297.9
3.16-3.652.20.1390.1053.838796175030.090.1390.1059.798.2
3.65-4.472.20.1230.0933.832884148410.080.1230.09311.698.5
4.47-6.322.20.1190.0913.425309114850.0760.1190.09111.698.5
6.32-19.9982.10.0950.07351306761090.060.0950.07311.395.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 2→19.998 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8627 / SU ML: 0.29 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 9828 5.01 %RANDOM
Rwork0.1877 ---
obs0.1895 196115 96.61 %-
all-196115 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.719 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 86.13 Å2 / Biso mean: 27.1496 Å2 / Biso min: 5.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.0453 Å2-1.1391 Å26.2012 Å2
2--3.2974 Å23.9338 Å2
3----2.2521 Å2
Refinement stepCycle: LAST / Resolution: 2→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15762 0 1223 1522 18507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01817326
X-RAY DIFFRACTIONf_angle_d1.11822833
X-RAY DIFFRACTIONf_chiral_restr0.0742227
X-RAY DIFFRACTIONf_plane_restr0.0042997
X-RAY DIFFRACTIONf_dihedral_angle_d16.9596473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2-2.02280.29772500.252846904940494073
2.0228-2.04650.2863070.245861886495649596
2.0465-2.07150.29262930.249561626455645597
2.0715-2.09770.2743310.229962656596659696
2.0977-2.12520.26143330.224961456478647897
2.1252-2.15430.27313290.206562606589658996
2.1543-2.1850.24692960.205261816477647797
2.185-2.21760.24833410.196462156556655697
2.2176-2.25220.24673400.213662866626662697
2.2522-2.28910.27193450.210761916536653697
2.2891-2.32850.23573520.196761976549654997
2.3285-2.37080.25463630.200361946557655798
2.3708-2.41630.26063420.207262726614661497
2.4163-2.46560.25143210.198362356556655697
2.4656-2.51910.24683090.187262616570657098
2.5191-2.57750.23093340.178462956629662998
2.5775-2.64190.23423270.181962516578657897
2.6419-2.71310.2443370.184762646601660198
2.7131-2.79280.21833100.180762986608660898
2.7928-2.88260.22473350.177962676602660298
2.8826-2.98540.22793210.178663086629662998
2.9854-3.10450.20913420.178863036645664598
3.1045-3.24520.20093240.168163146638663898
3.2452-3.41550.213220.172462956617661798
3.4155-3.62830.20263580.17163006658665898
3.6283-3.90650.20393160.172263516667666798
3.9065-4.29610.20433410.15963166657665799
4.2961-4.90970.16813170.154863416658665898
4.9097-6.15570.20253270.185463616688668898
6.1557-19.99860.24193650.242162816646664699
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)
10.2185-0.0148-0.0270.13730.05750.199-0.0054-0.02020.0081-0.0170.0122-0.0064-0.0129-0.0117-00.03960.0072-0.01140.0341-0.00520.0418-29.7206-24.4738-17.1488
20.17170.11890.02570.17570.00920.2076-0.0290.0650.0056-0.03750.0374-0.0057-0.03630.0408-00.0789-0.02230.00140.09520.01950.0337-12.7945-22.5888-51.639
300.0357-0.10270-0.10690.1909-0.02980.0127-0.0588-0.01570.0071-0.01030.00070.0039-00.0494-0.001-0.00440.0451-0.01830.0721-20.6428-56.7933-35.9238
40.2113-0.0189-0.04150.13460.10040.2061-0.0189-0.0201-0.05250.01920.00490.02540.00160.013100.04140.0054-0.0030.04440.01190.059817.904-99.820112.5608
500.0923-0.10570-0.10350.16720.00720.02490.01260.02790.0140.0242-0.02870.018100.0367-0.0046-0.00890.03590.0030.051427.2052-67.4758-6.1432
60.16580.0035-0.00520.2071-0.1570.28670.0366-0.0413-0.00020.05310.02980.0428-0.0968-0.0211-00.10530.01710.040.0618-0.01520.05389.7513-65.561928.0477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA1 - 340
2X-RAY DIFFRACTION2CHAIN BB1 - 340
3X-RAY DIFFRACTION3CHAIN CC1 - 340
4X-RAY DIFFRACTION4CHAIN DD1 - 340
5X-RAY DIFFRACTION5CHAIN EE1 - 340
6X-RAY DIFFRACTION6CHAIN FF1 - 340

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