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- PDB-2fbo: Crystal Structure of the Two Tandem V-type Regions of VCBP3 (v-re... -

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Basic information

Entry
Database: PDB / ID: 2fbo
TitleCrystal Structure of the Two Tandem V-type Regions of VCBP3 (v-region-containing chitin binding protein) to 1.85 A
Componentsvariable region-containing chitin-binding protein 3
KeywordsIMMUNE SYSTEM / immunoglobulin / VCBP / chitin binding protein / v-type / v set
Function / homology
Function and homology information


chitinase / chitinase activity / chitin binding / extracellular region / membrane
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHernandez Prada, J.A. / Haire, R.N. / Jakoncic, J. / Cannon, J.P. / Litman, G.W. / Ostrov, D.A.
CitationJournal: Nat.Immunol. / Year: 2006
Title: Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus
Authors: Hernandez Prada, J.A. / Haire, R.N. / Allaire, M. / Jakoncic, J. / Stojanoff, V. / Cannon, J.P. / Litman, G.W. / Ostrov, D.A.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: variable region-containing chitin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)27,2881
Polymers27,2881
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.597, 109.597, 48.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein variable region-containing chitin-binding protein 3 / VCBP3 tandem V regions / V1V2


Mass: 27288.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8I9N0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 1.7M Na Formate, 100 mM Na citrate, 200 mM MgCl, step soaking into 20% ethylene glycol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9192 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2005 / Details: mirror
RadiationMonochromator: Si111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9192 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Number: 52447 / Rmerge(I) obs: 0.053 / Χ2: 1.164 / D res high: 1.87 Å / D res low: 30 Å / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.073099.110.0381.5566.2
4.035.0799.810.041.5766.4
3.524.0310010.0421.6066.4
3.23.5210010.0451.5566.5
2.973.210010.0491.4336.5
2.792.9710010.0591.2076.5
2.652.7910010.0651.1546.5
2.542.6510010.0751.0846.5
2.442.5410010.0851.0726.5
2.362.4410010.091.056.5
2.282.3610010.1041.0226.5
2.222.2810010.1081.0386.5
2.162.2210010.1260.9646.5
2.112.1610010.1470.9716.4
2.062.1110010.1630.9286.2
2.012.0610010.180.925.8
1.972.0199.910.2010.9265.1
1.941.9798.210.2060.8554
1.91.9490.610.2210.8543.1
1.871.97710.2480.8092.6
ReflectionResolution: 1.85→20 Å / Num. obs: 28179 / % possible obs: 97.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.074 / Χ2: 0.988
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.8830.33212270.48884.3
1.88-1.923.60.30912430.55889.4
1.92-1.9540.25813080.55190
1.95-1.994.40.25313720.51896.9
1.99-2.044.80.25914030.50897.6
2.04-2.085.60.29814070.67499.6
2.08-2.146.90.2714300.55699.3
2.14-2.198.60.27114290.609100
2.19-2.2610.60.26414290.69199.9
2.26-2.3312.90.25314460.69499.9
2.33-2.4114.80.2214130.747100
2.41-2.5115.70.20614430.808100
2.51-2.6215.80.17614330.874100
2.62-2.7615.80.13414291.037100
2.76-2.9315.70.10614461.178100
2.93-3.1615.20.08114601.331100
3.16-3.4814.50.06314321.42100
3.48-3.9814.40.05314581.388100
3.98-514.30.04614741.301100
5-2014.20.0414971.2299.9

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se19.7830.1210.48400.462
2Se43.3950.9250.3460.10.441
Phasing dmFOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.61 / Reflection: 25970 / Reflection acentric: 24673 / Reflection centric: 1297
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.3-28.7680.930.940.8812311047184
3.3-5.30.930.940.8236863395291
2.7-3.30.810.810.6645534298255
2.3-2.70.630.640.5245334338195
2-2.30.420.430.3778377560277
1.9-20.20.20.24130403595

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.85→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1275 4.4 %Random
Rwork0.228 ---
all0.239 28165 --
obs0.239 28165 97.8 %-
Solvent computationBsol: 107.977 Å2
Displacement parametersBiso mean: 31.314 Å2
Baniso -1Baniso -2Baniso -3
1--2.577 Å2-2.56 Å20 Å2
2---2.577 Å20 Å2
3---5.153 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 0 277 2168
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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