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- PDB-3t0x: Fluorogen Activating Protein M8VLA4(S55P) in complex with dimethy... -

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Basic information

Entry
Database: PDB / ID: 3t0x
TitleFluorogen Activating Protein M8VLA4(S55P) in complex with dimethylindole red
ComponentsImmunoglobulin variable lambda domain M8VLA4(S55P)
KeywordsDYE-BINDING PROTEIN / immunoglobulin fold / fluorogen activation / dimethylindole red
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-DIW
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / 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

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin variable lambda domain M8VLA4(S55P)
B: Immunoglobulin variable lambda domain M8VLA4(S55P)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,40911
Polymers26,4292
Non-polymers9809
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-9 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.494, 83.494, 76.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Immunoglobulin variable lambda domain M8VLA4(S55P)


Mass: 13214.251 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-DIW / 1-(3-sulfopropyl)-4-[(1E,3E)-3-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)prop-1-en-1-yl]quinolinium


Mass: 449.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N2O3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.25M ammonium sulfate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.722 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.722 Å / Relative weight: 1
ReflectionResolution: 1.96→37.34 Å / Num. all: 20018 / Num. obs: 20018 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 8.7 / Net I/σ(I): 35.5
Reflection shellResolution: 1.96→1.98 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 977 / Rsym value: 54.9 / % possible all: 100

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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: 1.96→37.3 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1048 5.25 %random
Rwork0.209 ---
obs0.2107 19963 99.6 %-
all-19963 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.727 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3927 Å2-0 Å2-0 Å2
2--0.3927 Å2-0 Å2
3----0.7855 Å2
Refinement stepCycle: LAST / Resolution: 1.96→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 65 136 1863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111805
X-RAY DIFFRACTIONf_angle_d1.4462456
X-RAY DIFFRACTIONf_dihedral_angle_d15.372635
X-RAY DIFFRACTIONf_chiral_restr0.086257
X-RAY DIFFRACTIONf_plane_restr0.008313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.05970.27961470.26622572X-RAY DIFFRACTION97
2.0597-2.18870.28371600.24172648X-RAY DIFFRACTION100
2.1887-2.35770.29591290.23612683X-RAY DIFFRACTION100
2.3577-2.59490.2811700.24612672X-RAY DIFFRACTION100
2.5949-2.97020.28321620.2232687X-RAY DIFFRACTION100
2.9702-3.74160.24281400.19742746X-RAY DIFFRACTION100
3.7416-37.34640.1861400.18022907X-RAY DIFFRACTION100
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)
10.0792-0.04460.03460.20410.06670.11440.02450.0179-0.0347-0.0814-0.0172-0.009-0.0653-0.0771-0.06330.18240.01020.01060.1078-0.05120.140425.44247.9937-14.2318
20.4199-0.2841-0.10730.6837-0.15620.6713-0.0838-0.0347-0.01450.8459-0.4985-0.250.0751-0.0015-0.74020.473-0.0857-0.0282-0.1328-0.01830.129422.0525-12.7106-2.2287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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