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- PDB-4d64: Structure of porin Omp-Pst1 from P. stuartii; the crystallographi... -

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Basic information

Entry
Database: PDB / ID: 4d64
TitleStructure of porin Omp-Pst1 from P. stuartii; the crystallographic symmetry generates a dimer of trimers.
ComponentsPORIN 1
KeywordsTRANSPORT PROTEIN / BACTERIAL JUNCTION / STERIC-ZIPPER / DIMER OF TRIMERS
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. / 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
Biological speciesPROVIDENCIA STUARTII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNasrallah, C. / Colletier, J.P.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Porin self-association enables cell-to-cell contact inProvidencia stuartiifloating communities.
Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / ...Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / Winterhalter, M. / Colletier, J.P.
#1: Journal: Plos One / Year: 2015
Title: Understanding Voltage Gating of Providencia Stuartii Porins at Atomic Level.
Authors: Song, W. / Bajaj, H. / Nasrallah, C. / Jiang, H. / Winterhalter, M. / Colletier, J. / Xu, Y.
History
DepositionNov 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PORIN 1
B: PORIN 1
C: PORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1444
Polymers117,1043
Non-polymers401
Water2,882160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-44.9 kcal/mol
Surface area42160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.520, 142.020, 113.320
Angle α, β, γ (deg.)90.00, 131.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN C
211CHAIN A
311CHAIN B

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Components

#1: Protein PORIN 1 /


Mass: 39034.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROVIDENCIA STUARTII (bacteria) / Plasmid: PG_OMP-PST1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DELTA-OMP8 / References: UniProt: E3U904
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.94 Å3/Da / Density % sol: 68.8 % / Description: NONE
Crystal growpH: 6.5
Details: 14% PEG6000 MME, 0.1 M BUFFER MES PH6.5, 0.1 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 27279 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 2.68 % / Biso Wilson estimate: 53.11 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.98
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODELLER-MODEL OF OMP-PST1 BASED ON PDB ENTRY 1OPF

1opf


Resolution: 3.2→36.254 Å / SU ML: 0.99 / σ(F): 1.99 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 1364 5 %
Rwork0.2075 --
obs0.2102 27270 91.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 3.913 Å2 / ksol: 0.236 e/Å3
Displacement parametersBiso mean: 43.916 Å2
Baniso -1Baniso -2Baniso -3
1-9.412 Å20 Å219.1876 Å2
2---8.4621 Å20 Å2
3----0.9499 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8271 0 1 160 8432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068472
X-RAY DIFFRACTIONf_angle_d1.00711444
X-RAY DIFFRACTIONf_dihedral_angle_d15.2433022
X-RAY DIFFRACTIONf_chiral_restr0.0741158
X-RAY DIFFRACTIONf_plane_restr0.0041526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2721X-RAY DIFFRACTIONPOSITIONAL
12A2721X-RAY DIFFRACTIONPOSITIONAL0.051
13B2739X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31430.3851390.30272657X-RAY DIFFRACTION93
3.3143-3.44690.31021390.2632636X-RAY DIFFRACTION93
3.4469-3.60360.31370.232597X-RAY DIFFRACTION92
3.6036-3.79340.30241360.20862591X-RAY DIFFRACTION92
3.7934-4.03080.25561380.19982622X-RAY DIFFRACTION92
4.0308-4.34160.24561370.18042605X-RAY DIFFRACTION92
4.3416-4.77760.22091360.15972567X-RAY DIFFRACTION91
4.7776-5.46690.21121360.16412596X-RAY DIFFRACTION91
5.4669-6.880.24651350.20282555X-RAY DIFFRACTION90
6.88-36.25650.24181310.22942480X-RAY DIFFRACTION86
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)
12.3834-0.48631.17171.651-0.1641.1927-0.02180.3802-0.059-0.1582-0.0338-0.0490.3962-0.10830.11630.6034-0.02530.00430.65040.01360.4441-22.565630.357211.3822
21.79560.2561.26581.14430.15972.0044-0.174-0.1833-0.27270.04790.0444-0.07410.5233-0.12710.15820.8639-0.00220.13320.64660.01130.6586-26.582512.899918.8737
31.6781-0.05190.22322.2821-0.76552.00150.2079-0.19390.10980.05180.07660.5937-0.0441-0.2232-0.26470.6549-0.122-0.0360.77-0.16790.5675-41.59720.60619.6254
42.0451-0.55010.79871.8130.03820.62370.0896-0.0050.20550.09020.12740.03850.06630.2323-0.18110.45010.0679-0.04960.7758-0.04790.4903-9.816938.294820.2448
51.4887-0.9282-0.25362.08710.28991.1162-0.1077-0.4488-0.00320.39080.1876-0.1390.05970.5792-0.09710.50320.0121-0.08521.00260.01150.5367-1.506341.233636.1315
62.57910.65531.77752.35230.61791.8256-0.1780.3448-0.154-0.48350.3064-0.4252-0.09450.8983-0.15250.5728-0.10710.12390.72920.02240.6894-22.078848.438711.8144
71.05050.44810.05951.982-0.32821.54660.2696-0.07560.39660.1923-0.13570.4134-0.2861-0.1872-0.08840.6580.02970.11270.58520.01590.7166-35.205860.116913.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:86)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 87:260)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 261:352)
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 1:86)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 87:352)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1:86)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 87:352)

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