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- PDB-5o9c: Crystal structure of Omp36 from Enterobacter aerogenes -

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Basic information

Entry
Database: PDB / ID: 5o9c
TitleCrystal structure of Omp36 from Enterobacter aerogenes
ComponentsOsmoporin Omp36
KeywordsMEMBRANE PROTEIN / Beta-barrell / outer-membrane / channel / porin
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
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
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.469 Å
AuthorsFerrara, L. / Naismith, J.
CitationJournal: To Be Published
Title: Crystal structure of Omp36 from Enterobacter aerogenes
Authors: Ferrara, L. / Naismith, J.
History
DepositionJun 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Osmoporin Omp36
A: Osmoporin Omp36
D: Osmoporin Omp36
B: Osmoporin Omp36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,5438
Polymers157,3174
Non-polymers1,2264
Water1,76598
1
C: Osmoporin Omp36

C: Osmoporin Omp36

C: Osmoporin Omp36


Theoretical massNumber of molelcules
Total (without water)117,9883
Polymers117,9883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area9080 Å2
ΔGint-44 kcal/mol
Surface area41500 Å2
MethodPISA
2
D: Osmoporin Omp36
hetero molecules

D: Osmoporin Omp36
hetero molecules

D: Osmoporin Omp36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9076
Polymers117,9883
Non-polymers9193
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area10940 Å2
ΔGint-43 kcal/mol
Surface area40710 Å2
MethodPISA
3
B: Osmoporin Omp36
hetero molecules

B: Osmoporin Omp36
hetero molecules

B: Osmoporin Omp36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8269
Polymers117,9883
Non-polymers1,8396
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Buried area13230 Å2
ΔGint-33 kcal/mol
Surface area40940 Å2
MethodPISA
4
A: Osmoporin Omp36
hetero molecules

A: Osmoporin Omp36
hetero molecules

A: Osmoporin Omp36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9076
Polymers117,9883
Non-polymers9193
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area10080 Å2
ΔGint-59 kcal/mol
Surface area41510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.098, 125.098, 126.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11D-512-

HOH

21D-518-

HOH

31B-513-

HOH

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Components

#1: Protein
Osmoporin Omp36


Mass: 39329.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: omp36 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9ALY0
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.63 Å3/Da / Density % sol: 66.15 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.46→56.073 Å / Num. obs: 79038 / % possible obs: 99.27 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.469→56.073 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.58 / Phase error: 23.46
RfactorNum. reflection% reflection
Rfree0.2394 3923 4.97 %
Rwork0.1934 --
obs0.1957 79012 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.469→56.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10924 0 71 98 11093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711227
X-RAY DIFFRACTIONf_angle_d0.96515167
X-RAY DIFFRACTIONf_dihedral_angle_d8.7866395
X-RAY DIFFRACTIONf_chiral_restr0.0551536
X-RAY DIFFRACTIONf_plane_restr0.0052028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4689-2.49910.31171160.19772740X-RAY DIFFRACTION100
2.4991-2.53070.25041580.18592684X-RAY DIFFRACTION100
2.5307-2.5640.2471140.17322694X-RAY DIFFRACTION100
2.564-2.59910.23631400.16532661X-RAY DIFFRACTION100
2.5991-2.63620.25891440.16562705X-RAY DIFFRACTION100
2.6362-2.67560.22821220.172739X-RAY DIFFRACTION100
2.6756-2.71740.23431560.16652691X-RAY DIFFRACTION99
2.7174-2.76190.23921060.17432661X-RAY DIFFRACTION99
2.7619-2.80960.25961500.17072701X-RAY DIFFRACTION100
2.8096-2.86070.25581550.18112701X-RAY DIFFRACTION100
2.8607-2.91570.25621240.19172732X-RAY DIFFRACTION100
2.9157-2.97520.26581580.18742679X-RAY DIFFRACTION100
2.9752-3.03990.23671640.17672636X-RAY DIFFRACTION100
3.0399-3.11060.23721400.18152681X-RAY DIFFRACTION100
3.1106-3.18840.24761220.19532702X-RAY DIFFRACTION100
3.1884-3.27460.23941600.19672684X-RAY DIFFRACTION100
3.2746-3.37090.26881360.18152686X-RAY DIFFRACTION100
3.3709-3.47970.20311280.20652700X-RAY DIFFRACTION100
3.4797-3.6040.23291520.20292664X-RAY DIFFRACTION99
3.604-3.74830.2511500.20652654X-RAY DIFFRACTION99
3.7483-3.91890.29451120.20862723X-RAY DIFFRACTION99
3.9189-4.12540.19451480.18912681X-RAY DIFFRACTION99
4.1254-4.38380.20511640.18232625X-RAY DIFFRACTION99
4.3838-4.72210.24371300.17542673X-RAY DIFFRACTION99
4.7221-5.1970.22011600.1822681X-RAY DIFFRACTION99
5.197-5.94830.22421440.20672655X-RAY DIFFRACTION99
5.9483-7.49140.24211420.23812630X-RAY DIFFRACTION98
7.4914-56.08740.26911280.26842626X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 93.951 Å / Origin y: 109.7339 Å / Origin z: 54.0587 Å
111213212223313233
T0.0479 Å2-0.0132 Å2-0.002 Å2-0.0592 Å20.0142 Å2--0.0512 Å2
L0.0116 °2-0.0552 °2-0.0015 °2--0.0271 °20.0149 °2---0.0007 °2
S-0.0032 Å °-0.0111 Å °-0.01 Å °-0.0211 Å °0.0104 Å °-0.0217 Å °-0.0119 Å °0.0228 Å °-0.0037 Å °
Refinement TLS groupSelection details: all

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