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- PDB-4be5: V. cholera biofilm scaffolding protein RbmA -

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Basic information

Entry
Database: PDB / ID: 4be5
TitleV. cholera biofilm scaffolding protein RbmA
ComponentsRBMA
KeywordsCELL ADHESION / BACTERIAL COMMUNITY / SCAFFOLDING
Function / homologyImmunoglobulin-like - #3880 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesVIBRIO CHOLERAE MJ-1236 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsMaestre-Reyna, M. / Wang, A.H.-J.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights Into Rbma, a Biofilm Scaffolding Protein of V. Cholerae.
Authors: Maestre-Reyna, M. / Wu, W. / Wang, A.H.
History
DepositionMar 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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: RBMA
B: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5995
Polymers57,3922
Non-polymers2073
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-30.7 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.888, 118.888, 104.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-2162-

HOH

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Components

#1: Protein RBMA


Mass: 28696.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE MJ-1236 (bacteria) / Variant: SEROTYPE O1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3NSJ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.22 Å3/Da / Density % sol: 61.82 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M BIS/TRIS, PH 6.5, 1.5 M NACL

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.529
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2012 / Details: MIRRORS
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.529 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 27736 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 45.4
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 9.74 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.46→24.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.366 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23434 1395 5 %RANDOM
Rwork0.1828 ---
obs0.18543 26340 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.537 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.46→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 13 304 3799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023653
X-RAY DIFFRACTIONr_bond_other_d0.0010.023420
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9474970
X-RAY DIFFRACTIONr_angle_other_deg0.74137854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17125.854164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35715583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1821511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02831
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.462→2.525 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 92 -
Rwork0.25 1902 -
obs--98.62 %
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)
10.12290.1004-0.00413.2621-1.25151.2772-0.04440.09250.0122-0.30440.08850.09230.13-0.1944-0.04410.0644-0.0324-0.0360.11490.0060.026442.478122.55697.6166
20.4696-0.0969-0.02881.23490.67760.68990.0891-0.0574-0.04910.1599-0.080.0130.06860.0258-0.00910.0673-0.00970.00580.08040.03230.023469.058929.596729.8086
30.2030.1564-0.11911.21170.03630.3317-0.05450.0541-0.0271-0.0222-0.01030.0568-0.040.00060.06480.07040.00040.0070.06340.02740.048566.658432.805910.8858
40.2558-0.0172-0.28670.6331-0.06280.39050.01610.0250.05360.0257-0.0257-0.00010.0045-0.06160.00960.02880.01040.04160.0675-0.00250.11941.538428.539826.7343
539.83128.4867-13.91844.63740.948610.2811-0.64032.0382-0.3111-0.38660.8089-0.2793-0.1307-0.2169-0.16870.1274-0.0182-0.0160.1793-0.05450.049253.765639.1486-0.859
622.87363.7219-6.82610.6428-1.41944.62390.3051-2.0510.13230.0044-0.32010.02270.28310.63740.0150.0605-0.01260.02790.20940.04050.108650.62640.805737.2432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 151
2X-RAY DIFFRACTION2B38 - 151
3X-RAY DIFFRACTION3A159 - 271
4X-RAY DIFFRACTION4B159 - 271
5X-RAY DIFFRACTION5A152 - 158
6X-RAY DIFFRACTION6B152 - 158

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