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- PDB-1uun: Main porin from Mycobacterium smegmatis (MspA) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1uun
TitleMain porin from Mycobacterium smegmatis (MspA)
ComponentsMSPA
KeywordsPORIN / MYCOBACTERIA
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / iron ion transport / extracellular region
Similarity search - Function
Porin MspA ribbon fold / Porin MspA ribbon domain / Porin MspA (Ig-like beta-sandwich domain) / Porin family, mycobacterial-type / MspA / Leukocidin/porin MspA superfamily / Ribbon / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Porin MspA / Porin MspA
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsFaller, M. / Niederweis, M. / Schulz, G.E.
CitationJournal: Science / Year: 2004
Title: The Structure of a Mycobacterial Outer-Membrane Channel
Authors: Faller, M. / Niederweis, M. / Schulz, G.E.
History
DepositionJan 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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: MSPA
B: MSPA


Theoretical massNumber of molelcules
Total (without water)38,9992
Polymers38,9992
Non-polymers00
Water1,71195
1
A: MSPA
B: MSPA

A: MSPA
B: MSPA

A: MSPA
B: MSPA

A: MSPA
B: MSPA


Theoretical massNumber of molelcules
Total (without water)155,9968
Polymers155,9968
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.860, 113.860, 229.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.708152, 0.70606, -0.000181), (-0.706059, 0.708152, 0.001367), (0.001093, -0.00084, 0.999999)
Vector: 0.0092, -0.1538, 0.0219)

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Components

#1: Protein MSPA


Mass: 19499.516 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-211 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Plasmid: PMN501 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9RLP7, UniProt: A0QR29*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, ARG 123 FROM ALA ENGINEERED MUTATION IN CHAIN B, ARG 123 FROM ALA

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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: 4.75 Å3/Da / Density % sol: 74 %
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM: 0.1M SODIUM CITRATE PH 5.6, 0.1M LITHIUM SULFATE, 12% PEG4000, DETERGENTS WERE ADDED
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
160 mMsodium citrate1droppH5.6
260 mM1dropLi2SO4
37 %(w/v)PEG40001drop
40.2 %(w/v)1dropC8E4
535 mMC-HEGA-101drop
66 mg/mlMspA1drop
70.1 Msodium citrate1reservoirpH5.6
80.1 M1reservoirLi2SO4
912 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 25527 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.8 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 6.3 / % possible all: 89
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.8 Å / % possible obs: 89 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.3

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.2 Å / SU B: 6.964 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.219
RfactorNum. reflection% reflectionSelection details
Rfree0.24924 1298 5.1 %RANDOM
Rwork0.22611 ---
obs0.22729 24195 98 %-
Displacement parametersBiso mean: 39.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 0 95 2853
Refinement
*PLUS
Lowest resolution: 29 Å / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.6

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