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- PDB-4kkr: Crystal structure of Vibrio cholerae RbmA (crystal form 3) -

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Basic information

Entry
Database: PDB / ID: 4kkr
TitleCrystal structure of Vibrio cholerae RbmA (crystal form 3)
ComponentsRbmA protein
KeywordsSTRUCTURAL PROTEIN / Fn-III / matrix protein / secreted
Function / homologyImmunoglobulin-like - #3880 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSondermann, H. / Giglio, K.M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Structural Basis for Biofilm Formation via the Vibrio cholerae Matrix Protein RbmA.
Authors: Giglio, K.M. / Fong, J.C. / Yildiz, F.H. / Sondermann, H.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 protein
B: RbmA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8233
Polymers52,7872
Non-polymers351
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-34 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.404, 119.404, 104.025
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
11A-324-

HOH

21A-438-

HOH

31B-620-

HOH

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Components

#1: Protein RbmA protein


Mass: 26393.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: MJ-1236 / Gene: VCD_003406 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3NSJ9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS, 3.0 M NaCl, 25% Xylitol, 0.16% Thiamine monophosphate chlroide dihydrate, 0.16% Acetylsalicylic acid, 0.16% Cholic acid, 0.16% 1,2,3-Heptanetriol, 0.16% Vanillin, 0.16% N- ...Details: 0.1 M BIS-TRIS, 3.0 M NaCl, 25% Xylitol, 0.16% Thiamine monophosphate chlroide dihydrate, 0.16% Acetylsalicylic acid, 0.16% Cholic acid, 0.16% 1,2,3-Heptanetriol, 0.16% Vanillin, 0.16% N-Acetly-D-mannosamine, 0.02 M HEPES sodium, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 51263 / Num. obs: 51215 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.284 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 2000 3.91 %random
Rwork0.1607 ---
obs0.1619 51184 99.81 %-
all-51263 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 1 568 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073640
X-RAY DIFFRACTIONf_angle_d1.0424950
X-RAY DIFFRACTIONf_dihedral_angle_d13.181334
X-RAY DIFFRACTIONf_chiral_restr0.082554
X-RAY DIFFRACTIONf_plane_restr0.004650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.23461390.18343442X-RAY DIFFRACTION100
2.05-2.10540.21071410.16613451X-RAY DIFFRACTION100
2.1054-2.16740.21411410.16583469X-RAY DIFFRACTION100
2.1674-2.23730.22241400.16553441X-RAY DIFFRACTION100
2.2373-2.31730.21861410.17183474X-RAY DIFFRACTION100
2.3173-2.41010.19491420.16733473X-RAY DIFFRACTION100
2.4101-2.51970.21351420.16613496X-RAY DIFFRACTION100
2.5197-2.65260.19491420.17613495X-RAY DIFFRACTION100
2.6526-2.81870.21041420.18273506X-RAY DIFFRACTION100
2.8187-3.03630.23841420.18283508X-RAY DIFFRACTION100
3.0363-3.34180.20211440.16423538X-RAY DIFFRACTION100
3.3418-3.82510.16731440.14273552X-RAY DIFFRACTION100
3.8251-4.81830.15591460.12483598X-RAY DIFFRACTION100
4.8183-44.29490.16831540.1723741X-RAY DIFFRACTION99
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)
12.24810.6134-1.21921.47710.29881.830900.55210.2944-0.25020.03690.1137-0.2944-0.2125-0.00370.2350.00970.00940.25070.07590.1699-36.416716.9118-18.9653
21.0993-0.05120.25540.81880.0011.1659-0.00710.120.0517-0.079-0.0394-0.01350.02740.14460.05020.12630.0030.0170.13540.00270.1079-26.6592-6.9668-15.6147
31.45550.24680.97611.62950.08261.44650.0448-0.2077-0.00770.18640.01820.18550.1346-0.1484-0.06630.1582-0.00530.02970.16410.01330.1308-29.4387-9.8934.2233
42.5790.33510.20241.1937-0.04381.3141-0.0421-0.2358-0.12190.05050.0250.02580.1022-0.0810.01570.19140.01090.03840.16890.01060.1287-29.7903-8.25464.1104
51.0723-0.4649-0.00170.84090.16881.3951-0.0558-0.06190.09490.03570.0562-0.1348-0.17510.15440.00940.16-0.0180.02330.1396-0.02510.1815-30.88817.71911.0278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 39:155)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 156:271)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 38:98)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 99:156)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 157:271)

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