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- PDB-3ls3: Padron0.9-ON (fluorescent state) -

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Basic information

Entry
Database: PDB / ID: 3ls3
TitlePadron0.9-ON (fluorescent state)
ComponentsPadron0.9
KeywordsFLUORESCENT PROTEIN / beta-barrel / cis-trans isomerisation
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / SPERMIDINE
Function and homology information
Biological speciesPectiniidae (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrakemann, T. / Weber, G. / Trowitzsch, S. / Wahl, M.C. / Jakobs, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Molecular basis of the light-driven switching of the photochromic fluorescent protein Padron.
Authors: Brakemann, T. / Weber, G. / Andresen, M. / Groenhof, G. / Stiel, A.C. / Trowitzsch, S. / Eggeling, C. / Grubmuller, H. / Hell, S.W. / Wahl, M.C. / Jakobs, S.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Padron0.9
B: Padron0.9
C: Padron0.9
D: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,31915
Polymers107,8944
Non-polymers1,42511
Water12,250680
1
A: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3034
Polymers26,9741
Non-polymers3293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2643
Polymers26,9741
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3564
Polymers26,9741
Non-polymers3833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3964
Polymers26,9741
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.855, 103.806, 121.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Padron0.9


Mass: 26973.525 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectiniidae (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H19N3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 35% PEG 400, 5% PEG 3000, 0.1M Hepes, 10% glycerol, 0.1M spermidine, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 109915 / Num. obs: 110246 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.036 / Net I/σ(I): 18.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 10889 / Rsym value: 0.618 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IOV

2iov


Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.649 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19996 5479 5 %RANDOM
Rwork0.16782 ---
obs0.16946 104188 99.31 %-
all-104912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.686 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---1.93 Å20 Å2
3---2.57 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6997 0 95 680 7772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217806
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.96310587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1625995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58924.301379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3471534
X-RAY DIFFRACTIONr_chiral_restr0.1090.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216078
X-RAY DIFFRACTIONr_mcbond_it0.7831.54607
X-RAY DIFFRACTIONr_mcangle_it1.47127481
X-RAY DIFFRACTIONr_scbond_it2.51433199
X-RAY DIFFRACTIONr_scangle_it4.0414.53065
LS refinement shellResolution: 1.65→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 412 -
Rwork0.293 7271 -
obs-7271 95.65 %
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)
11.015-0.0748-0.21941.17220.24131.16930.0437-0.25080.03820.241-0.0179-0.2592-0.04940.293-0.02580.1036-0.039-0.0830.161-0.00680.0953-17.14621.783-25.849
21.02410.3584-0.2240.95220.03860.4732-0.01980.0857-0.1755-0.060.0253-0.27490.00380.1091-0.00550.02560.00240.02640.0877-0.00030.1374-15.158.264-54.283
30.5683-0.18080.15621.32370.4760.7238-0.0039-0.12640.03670.2392-0.11250.29370.0694-0.08760.11640.1407-0.04250.04850.1284-0.0330.0803-47.80619.571-27.68
40.7199-0.03470.06541.1145-0.11290.60170.03560.0501-0.1041-0.0897-0.03670.1630.0685-0.00840.00110.0794-0.008-0.02610.07220.00060.0562-45.9833.18-54.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2B2 - 218
3X-RAY DIFFRACTION3C2 - 217
4X-RAY DIFFRACTION4D-8 - 218

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