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- PDB-3t0v: Unliganded fluorogen activating protein M8VL -

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Basic information

Entry
Database: PDB / ID: 3t0v
TitleUnliganded fluorogen activating protein M8VL
Componentsimmunoglobulin variable lambda domain
KeywordsDYE-BINDING PROTEIN / immunoglobulin fold / fluorogen activation / dimethylindole red
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-PE3
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsStanfield, R. / Senutovitch, N. / Bhattacharyya, S. / Rule, G. / Wilson, I.A. / Armitage, B. / Waggoner, A.S. / Berget, P.
CitationJournal: Biochemistry / Year: 2012
Title: A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red.
Authors: Senutovitch, N. / Stanfield, R.L. / Bhattacharyya, S. / Rule, G.S. / Wilson, I.A. / Armitage, B.A. / Waggoner, A.S. / Berget, P.B.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Apr 11, 2012Group: Database references
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: immunoglobulin variable lambda domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4828
Polymers13,2041
Non-polymers1,2777
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.663, 93.639, 30.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 1 types, 1 molecules A

#1: Antibody immunoglobulin variable lambda domain


Mass: 13204.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): MachTI

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Non-polymers , 6 types, 134 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M ammonium sulfate, 2% PEG 400, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→29.244 Å / Num. all: 21290 / Num. obs: 21290 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 4.3 / Net I/σ(I): 30.1
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 830 / Rsym value: 31.7 / % possible all: 79.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.451→29.2 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1090 5.12 %random
Rwork0.1793 ---
obs0.1808 21280 97.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.32 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8572 Å2-0 Å2-0 Å2
2---1.2616 Å2-0 Å2
3----2.5956 Å2
Refinement stepCycle: LAST / Resolution: 1.451→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 51 127 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006947
X-RAY DIFFRACTIONf_angle_d1.1211284
X-RAY DIFFRACTIONf_dihedral_angle_d10.659356
X-RAY DIFFRACTIONf_chiral_restr0.075137
X-RAY DIFFRACTIONf_plane_restr0.004163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.451-1.51650.28691120.25732135X-RAY DIFFRACTION84
1.5165-1.59650.25011380.18882474X-RAY DIFFRACTION98
1.5965-1.69650.23571200.18012572X-RAY DIFFRACTION100
1.6965-1.82750.25971540.18052533X-RAY DIFFRACTION100
1.8275-2.01130.22991410.18792550X-RAY DIFFRACTION100
2.0113-2.30230.20741470.17162581X-RAY DIFFRACTION100
2.3023-2.90020.19721480.1772600X-RAY DIFFRACTION100
2.9002-29.250.18531300.17412745X-RAY DIFFRACTION100

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