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- PDB-5j75: Fluorogen Activating Protein AM2.2 in complex with ML342 -

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Basic information

Entry
Database: PDB / ID: 5j75
TitleFluorogen Activating Protein AM2.2 in complex with ML342
ComponentsscFv AM2.2
KeywordsIMMUNE SYSTEM / fluorogen activating protein / drug discovery / biosensor / protein trafficking
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-6GQ / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStanfield, R.L. / Wilson, I.A. / Wu, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1U54MH084690-02 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)5U54MH084690-03 CDP2 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)U54MH084659 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5U54RR022241 United States
CitationJournal: J Biomol Screen / Year: 2016
Title: Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair.
Authors: Wu, Y. / Stauffer, S.R. / Stanfield, R.L. / Tapia, P.H. / Ursu, O. / Fisher, G.W. / Szent-Gyorgyi, C. / Evangelisti, A. / Waller, A. / Strouse, J.J. / Carter, M.B. / Bologa, C. / Gouveia, K. ...Authors: Wu, Y. / Stauffer, S.R. / Stanfield, R.L. / Tapia, P.H. / Ursu, O. / Fisher, G.W. / Szent-Gyorgyi, C. / Evangelisti, A. / Waller, A. / Strouse, J.J. / Carter, M.B. / Bologa, C. / Gouveia, K. / Poslusney, M. / Waggoner, A.S. / Lindsley, C.W. / Jarvik, J.W. / Sklar, L.A.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 24, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv AM2.2
B: scFv AM2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6728
Polymers54,5162
Non-polymers1,1576
Water1,17165
1
A: scFv AM2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8364
Polymers27,2581
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: scFv AM2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8364
Polymers27,2581
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.021, 72.415, 64.562
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 2 - 254 / Label seq-ID: 2 - 254

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Antibody scFv AM2.2


Mass: 27257.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia (fungus)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-6GQ / N,4-dimethyl-N-{2-oxo-2-[4-(pyridin-2-yl)piperazin-1-yl]ethyl}benzene-1-sulfonamide


Mass: 388.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 0.2M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→50.01 Å / Num. obs: 31546 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.4 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J74

5j74


Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.224 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26295 1737 5.5 %RANDOM
Rwork0.22147 ---
obs0.22378 29736 96.26 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 37.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.23 Å2
2--1 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 74 65 3595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193610
X-RAY DIFFRACTIONr_bond_other_d0.0040.023220
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9414920
X-RAY DIFFRACTIONr_angle_other_deg1.17237440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71624.853136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61815532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2381510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214136
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02808
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_it1.8152.4111860
X-RAY DIFFRACTIONr_mcbond_other1.8152.4111861
X-RAY DIFFRACTIONr_mcangle_it3.023.5972320
X-RAY DIFFRACTIONr_mcangle_other3.0183.5992319
X-RAY DIFFRACTIONr_scbond_it2.0972.5991750
X-RAY DIFFRACTIONr_scbond_other2.0962.5991751
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2853.8192601
X-RAY DIFFRACTIONr_long_range_B_refined5.33419.0133769
X-RAY DIFFRACTIONr_long_range_B_other5.33419.0153770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24848 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 127 -
Rwork0.302 2168 -
obs--94.29 %
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)
12.6299-0.39070.35810.8091-0.93523.07040.04180.5416-0.2026-0.0419-0.00410.12770.0058-0.188-0.03770.0164-0.0156-0.01010.2416-0.03080.03530.5844-25.121281.9816
22.803-0.2069-0.17282.01190.52830.8466-0.10320.318-0.0873-0.01290.0924-0.1632-0.07580.01860.01080.0127-0.0189-0.0010.1599-0.00520.022221.7441-25.800785.8418
32.6588-0.0895-0.03561.23761.00233.5045-0.0251-0.5425-0.2720.06630.0701-0.117-0.04460.0965-0.04510.01070.0255-0.00750.22450.04280.04241.762-24.8758112.9925
43.59270.4192-0.02791.6564-0.18521.4304-0.105-0.4356-0.1399-0.02540.06570.0897-0.0468-0.09550.03930.0050.01780.00130.15270.01520.0147-19.4009-25.5408109.0839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 121
2X-RAY DIFFRACTION2A142 - 254
3X-RAY DIFFRACTION3B2 - 121
4X-RAY DIFFRACTION4B142 - 254

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