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- PDB-3mc9: POTRA1-2 of the periplasmic domain of Omp85 from Anabaena -

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Basic information

Entry
Database: PDB / ID: 3mc9
TitlePOTRA1-2 of the periplasmic domain of Omp85 from Anabaena
ComponentsAlr2269 protein
KeywordsMEMBRANE PROTEIN / Polypeptide transport associated / POTRA / outer bacterial membrane / protein membrane transport / beta barrel biogenesis
Function / homology
Function and homology information


Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / membrane protein fhac / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKoenig, P. / Schleiff, E. / Sinning, I. / Tews, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Conserved properties of polypeptide transport-associated (POTRA) domains derived from cyanobacterial Omp85.
Authors: Koenig, P. / Mirus, O. / Haarmann, R. / Sommer, M.S. / Sinning, I. / Schleiff, E. / Tews, I.
History
DepositionMar 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alr2269 protein
B: Alr2269 protein


Theoretical massNumber of molelcules
Total (without water)69,4452
Polymers69,4452
Non-polymers00
Water2,756153
1
A: Alr2269 protein


Theoretical massNumber of molelcules
Total (without water)34,7231
Polymers34,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr2269 protein


Theoretical massNumber of molelcules
Total (without water)34,7231
Polymers34,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-14 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.366, 108.366, 60.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Alr2269 protein


Mass: 34722.551 Da / Num. of mol.: 2 / Fragment: Periplasmic POTRA domains (Residues 161-467)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2269 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YUR6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY ...THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY DEGRADED TO A TRUNCATED SPECIES DURING THE CRYSTALLIZATION EXPERIMENT. THEREFORE, CALCULATED VM AND VS VALUES ARE BASED ON AN ESTIMATE. THE AUTHORS ASSUMED RESIDUES 161 TO 281 TO BE PRESENT.

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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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M calcium chloride, 20 % PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2009 / Details: SINGLE SILICON (111) MONOCHROMATOR
RadiationMonochromator: SINGLE SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23906 / % possible obs: 100 % / Observed criterion σ(I): -4 / Redundancy: 7.8 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.606 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY DEGRADED TO A TRUNCATED SPECIES DURING THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY DEGRADED TO A TRUNCATED SPECIES DURING THE CRYSTALLIZATION EXPERIMENT. THEREFORE, CALCULATED VM AND VS VALUES ARE BASED ON AN ESTIMATE. THE AUTHORS ASSUMED RESIDUES 161 TO 281 TO BE PRESENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1056 5.1 %RANDOM
Rwork0.195 ---
obs0.198 19600 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: 26.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.52 Å20 Å2
2---1.05 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 0 153 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222550
X-RAY DIFFRACTIONr_bond_other_d0.0010.021695
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9753480
X-RAY DIFFRACTIONr_angle_other_deg1.1134174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88325.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97215422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1331518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5831.51628
X-RAY DIFFRACTIONr_mcbond_other0.0981.5649
X-RAY DIFFRACTIONr_mcangle_it1.14422668
X-RAY DIFFRACTIONr_scbond_it1.8433922
X-RAY DIFFRACTIONr_scangle_it3.3334.5812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 80 -
Rwork0.224 1477 -
obs--100 %
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)
12.40221.28210.58932.24060.56470.8989-0.03640.0254-0.0708-0.03840.0334-0.1557-0.0124-0.01920.0030.0252-0.0111-0.00450.0062-0.00040.145147.953815.0815-7.7063
25.64810.9166-1.89561.424-0.34792.2828-0.25390.1554-0.18470.02320.2267-0.24430.1608-0.13920.02720.075-0.0127-0.0150.0762-0.05250.054525.1852-5.7911-13.0622
32.97320.29441.15811.2008-0.22951.19110.04720.0409-0.1803-0.04180.0164-0.1469-0.0676-0.0657-0.06370.12530.00150.01580.0762-0.01090.028817.1824-3.32597.7313
43.68071.632-0.57173.3769-1.95821.8789-0.054-0.1307-0.0992-0.0884-0.1493-0.1879-0.0010.11670.20330.0529-0.0135-0.04940.01810.02280.081447.41845.839212.5838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A217 - 296
2X-RAY DIFFRACTION2A297 - 381
3X-RAY DIFFRACTION3B217 - 296
4X-RAY DIFFRACTION4B297 - 381

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