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- PDB-4bei: V. cholera biofilm scaffolding protein RbmA in complex with 18-cr... -

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Basic information

Entry
Database: PDB / ID: 4bei
TitleV. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6
ComponentsRBMA
KeywordsCELL ADHESION / BACTERIAL COMMUNITY
Function / homologyImmunoglobulin-like - #3880 / Immunoglobulin-like / Sandwich / Mainly Beta / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesVIBRIO CHOLERAE MJ-1236 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Dec 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_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
C: RBMA
D: RBMA
E: RBMA
F: RBMA
G: RBMA
H: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,10820
Polymers229,5698
Non-polymers2,53912
Water5,206289
1
G: RBMA
H: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9214
Polymers57,3922
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-24.8 kcal/mol
Surface area19400 Å2
MethodPISA
2
C: RBMA
D: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0275
Polymers57,3922
Non-polymers6353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-23.1 kcal/mol
Surface area19420 Å2
MethodPISA
3
A: RBMA
B: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0275
Polymers57,3922
Non-polymers6353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-23.5 kcal/mol
Surface area19510 Å2
MethodPISA
4
E: RBMA
F: RBMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1336
Polymers57,3922
Non-polymers7414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-21.8 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.885, 136.885, 116.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
RBMA


Mass: 28696.119 Da / Num. of mol.: 8
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-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES PH 7 0.2 M CACL2 30 % (V/V) PEG 400 50 MM 18-CROWN-6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2012 / Details: MIRRORS
RadiationMonochromator: HORIZONTALLY FOCUSING SINGLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.6→22 Å / Num. obs: 75002 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.6
Reflection shellResolution: 2.6→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BE5

4be5


Resolution: 2.6→21.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.154 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26087 3781 5 %RANDOM
Rwork0.22172 ---
obs0.22368 71190 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.15 Å20 Å2
2--0.15 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14011 0 172 289 14472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214560
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213597
X-RAY DIFFRACTIONr_angle_refined_deg1.311.95219771
X-RAY DIFFRACTIONr_angle_other_deg1.3393.01131182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13751884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77425.826642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.473152238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521545
X-RAY DIFFRACTIONr_chiral_restr0.0710.22223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216959
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023302
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: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 274 -
Rwork0.341 5213 -
obs--99.98 %

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