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- PDB-2v9u: Rim domain of main porin from Mycobacteria smegmatis -

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Basic information

Entry
Database: PDB / ID: 2v9u
TitleRim domain of main porin from Mycobacteria smegmatis
ComponentsMSPA
KeywordsTRANSPORT PROTEIN / PORI / PORIN / MYCOBACTERIA
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / iron ion transport / extracellular region
Similarity search - Function
Porin MspA (Ig-like beta-sandwich domain) / Porin family, mycobacterial-type / MspA / Leukocidin/porin MspA superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Porin MspA / Porin MspA
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGrueninger, D. / Ziegler, M.O.P. / Koetter, J.W.A. / Treiber, N. / Schulze, M.-S. / Schulz, G.E.
Citation
#1: Journal: Science / Year: 2004
Title: The Structure of a Mycobacterial Outer-Membrane Channel
Authors: Faller, M. / Niederweis, M. / Schulz, G.E.
History
DepositionAug 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 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
C: MSPA
D: MSPA
E: MSPA
F: MSPA
G: MSPA
H: MSPA


Theoretical massNumber of molelcules
Total (without water)111,9638
Polymers111,9638
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14580 Å2
ΔGint-81.4 kcal/mol
Surface area52260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)139.377, 105.652, 102.963
Angle α, β, γ (deg.)90.00, 109.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MSPA


Mass: 13995.358 Da / Num. of mol.: 8 / Fragment: RIM DOMAIN, RESIDUES 28-96,149-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / 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.: 30 / 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: 3.2 Å3/Da / Density % sol: 61.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.59→65.79 Å / Num. obs: 36299 / % possible obs: 82.6 % / Observed criterion σ(I): 4.1 / Redundancy: 2.17 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.18
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.1 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→65.79 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.839 / SU B: 30.093 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.086 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1089 3 %RANDOM
Rwork0.273 ---
obs0.274 35210 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20.59 Å2
2--0.86 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.59→65.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7912 0 0 30 7942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0218080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.93911008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.44751048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46224.167384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.735151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.651556
X-RAY DIFFRACTIONr_chiral_restr0.1120.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.23220
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.25334
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.55324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27128208
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47833208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2854.52800
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 84
Rwork0.349 2722
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)
10.56770.7458-0.56712.2663-0.83741.78980.0728-0.11070.0247-0.0892-0.0889-0.0391-0.02320.07420.0161-0.0856-0.01730.012-0.08980.0042-0.0496-35.850531.5589.9292
21.47651.6986-0.50522.2029-0.39840.6748-0.1183-0.0668-0.0003-0.06730.0062-0.06770.0438-0.07680.1121-0.10790.04130.0066-0.0762-0.0329-0.0423-38.985755.79868.6244
33.23971.5192-0.45451.2545-0.1151.2515-0.0322-0.15710.0095-0.0386-0.08110.0586-0.08510.02730.1134-0.06150.0994-0.0188-0.0932-0.0498-0.0429-26.06475.622915.1394
42.1923-1.7951-0.44381.69210.50730.83840.02150.08290.1419-0.0171-0.2182-0.223-0.1297-0.12570.1967-0.0413-0.00990.00410.0055-0.0966-0.0802-4.607779.724625.9316
50.7449-1.5332-0.77583.27412.09022.8646-0.1707-0.2050.07520.09060.1086-0.24360.095-0.14040.0621-0.03-0.0415-0.0090.0904-0.0508-0.182313.10265.459634.9432
61.4609-0.47390.12832.33832.07762.330.073-0.1949-0.2718-0.03880.2643-0.131-0.3274-0.0292-0.33730.0561-0.0632-0.02770.11640.2064-0.158115.94541.274736.677
71.2010.7061.06010.73760.91032.56490.0539-0.203-0.26710.0535-0.1647-0.0916-0.10460.03250.1108-0.0407-0.0101-0.05160.09640.2304-0.07073.049921.278330.1052
81.9117-0.41560.72451.0005-1.84024.44250.0839-0.1612-0.3708-0.127-0.2134-0.07540.0280.30870.1295-0.1106-0.0327-0.0143-0.06220.0999-0.0255-18.362817.038818.8868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 184
2X-RAY DIFFRACTION2B1 - 184
3X-RAY DIFFRACTION3C1 - 184
4X-RAY DIFFRACTION4D1 - 184
5X-RAY DIFFRACTION5E1 - 184
6X-RAY DIFFRACTION6F1 - 184
7X-RAY DIFFRACTION7G1 - 184
8X-RAY DIFFRACTION8H1 - 184

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