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- PDB-4d65: Structure of porin Omp-Pst2 from P. stuartii; the asymmetric unit... -

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Basic information

Entry
Database: PDB / ID: 4d65
TitleStructure of porin Omp-Pst2 from P. stuartii; the asymmetric unit contains a dimer of trimers.
ComponentsPORIN 2
KeywordsTRANSPORT PROTEIN / STERIC-ZIPPER / BACTERIAL JUNCTION / DIMER OF TRIMERS
Function / homology
Function and homology information


porin activity / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Porin, gammaproteobacterial / 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
3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / Outer membrane porin protein OmpD
Similarity search - Component
Biological speciesPROVIDENCIA STUARTII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.1Oct 19, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Feb 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 1.3Apr 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: PORIN 2
B: PORIN 2
C: PORIN 2
D: PORIN 2
E: PORIN 2
F: PORIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,527185
Polymers227,6476
Non-polymers40,880179
Water56,1173115
1
A: PORIN 2
B: PORIN 2
C: PORIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,912117
Polymers113,8243
Non-polymers26,088114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: PORIN 2
E: PORIN 2
F: PORIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,61568
Polymers113,8243
Non-polymers14,79265
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.260, 135.510, 151.710
Angle α, β, γ (deg.)90.00, 114.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
PORIN 2 /


Mass: 37941.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROVIDENCIA STUARTII (bacteria) / Plasmid: PG_OMP-PST2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DELTA-OMP8 / References: UniProt: E3U905

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Non-polymers , 5 types, 3294 molecules

#2: Chemical...
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 165 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O3
#4: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3115 / 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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 8 / Details: 8% PEG 6000, 0.1 M TRIS PH 8, 1 M LICL

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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: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 279377 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 3.01 % / Biso Wilson estimate: 35.01 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.43
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.57 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 73.7

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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-PST2 BASED ON PDB ENTRY 4BD5

4bd5
PDB Unreleased entry


Resolution: 2.2→45.718 Å / SU ML: 0.25 / σ(F): 1.99 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 12465 5 %
Rwork0.1668 --
obs0.1683 249294 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODELLING
Displacement parametersBiso mean: 42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16074 0 2567 3115 21756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719154
X-RAY DIFFRACTIONf_angle_d1.425395
X-RAY DIFFRACTIONf_dihedral_angle_d13.4047751
X-RAY DIFFRACTIONf_chiral_restr0.1622477
X-RAY DIFFRACTIONf_plane_restr0.0043070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.35073120.33935929X-RAY DIFFRACTION71
2.225-2.25120.38453450.33656549X-RAY DIFFRACTION78
2.2512-2.27870.33363700.32117041X-RAY DIFFRACTION83
2.2787-2.30750.3063940.31017477X-RAY DIFFRACTION89
2.3075-2.33790.32734190.29087954X-RAY DIFFRACTION95
2.3379-2.36990.28944190.27437961X-RAY DIFFRACTION95
2.3699-2.40370.2964220.26458028X-RAY DIFFRACTION95
2.4037-2.43960.29294210.26057999X-RAY DIFFRACTION95
2.4396-2.47770.29154240.25658044X-RAY DIFFRACTION96
2.4777-2.51840.30824210.2458012X-RAY DIFFRACTION95
2.5184-2.56180.25134260.21918096X-RAY DIFFRACTION96
2.5618-2.60840.24694260.20948089X-RAY DIFFRACTION96
2.6084-2.65850.23814270.20248103X-RAY DIFFRACTION96
2.6585-2.71280.21344270.18638115X-RAY DIFFRACTION96
2.7128-2.77180.2144270.17438106X-RAY DIFFRACTION97
2.7718-2.83620.22754270.16918123X-RAY DIFFRACTION97
2.8362-2.90710.19364320.15848226X-RAY DIFFRACTION97
2.9071-2.98570.20034300.15068173X-RAY DIFFRACTION97
2.9857-3.07360.20614300.14388168X-RAY DIFFRACTION97
3.0736-3.17270.16754300.13668164X-RAY DIFFRACTION97
3.1727-3.28610.16344270.12918115X-RAY DIFFRACTION96
3.2861-3.41760.14784270.12398116X-RAY DIFFRACTION96
3.4176-3.57310.15544280.12428126X-RAY DIFFRACTION96
3.5731-3.76140.15734240.12288064X-RAY DIFFRACTION96
3.7614-3.9970.17164280.12958113X-RAY DIFFRACTION96
3.997-4.30540.14794160.13237933X-RAY DIFFRACTION94
4.3054-4.73820.14564200.12857966X-RAY DIFFRACTION94
4.7382-5.42290.17044190.14557969X-RAY DIFFRACTION94
5.4229-6.82860.19754180.16227947X-RAY DIFFRACTION93
6.8286-45.72780.18994290.18278123X-RAY DIFFRACTION94
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)
11.1855-0.08770.19180.73230.06040.98170.00220.02920.0573-0.0368-0.01770.1919-0.1086-0.09870.01040.1970.0539-0.02210.20180.0060.228514.510630.227914.3864
21.0747-0.0258-0.08950.7046-0.02371.11670.0047-0.00020.0932-0.0461-0.0295-0.2049-0.14470.12650.0290.1956-0.0540.02770.20830.04370.255152.893432.561613.0881
30.85080.08560.20810.77270.00121.1632-0.0486-0.12260.10550.3174-0.00650.0195-0.1598-0.01630.0180.35410.01440.00370.2343-0.04370.168634.869231.978446.9125
41.10440.0192-0.12760.649-0.05060.97910.02190.031-0.0935-0.0494-0.0182-0.19880.10420.1021-0.00730.18660.05220.02660.187-0.01590.231157.1113-23.68715.0607
50.9882-0.06750.19940.75750.06231.05470.0432-0.0357-0.1156-0.058-0.01680.19380.144-0.1284-0.01750.1929-0.0551-0.02550.2016-0.01350.261218.8472-26.080713.9375
60.90310.09760.03190.68850.04341.18820.0129-0.1762-0.10650.2587-0.0225-0.00430.1359-0.0201-0.01260.3147-0.0232-0.01480.23340.06370.171936.7508-24.499347.6246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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