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- PDB-3lsa: Padron0.9-OFF (non-fluorescent state) -

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Basic information

Entry
Database: PDB / ID: 3lsa
TitlePadron0.9-OFF (non-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: 1.79 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 / Refinement description / 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)109,27114
Polymers107,8944
Non-polymers1,37710
Water13,385743
1
A: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1192
Polymers26,9741
Non-polymers1451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4525
Polymers26,9741
Non-polymers4794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1583
Polymers26,9741
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Padron0.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5424
Polymers26,9741
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.334, 104.262, 123.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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)

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Non-polymers , 5 types, 753 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.6 %
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 / Wavelength: 1 Å
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 wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 83955 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.043
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 16753 / Rsym value: 0.502 / % possible all: 98.3

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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: 1.79→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.01 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19021 4433 5 %RANDOM
Rwork0.159 ---
obs0.1606 83955 99.18 %-
all-84649 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.79→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6971 0 89 743 7803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218017
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.96310908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29151022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27424.715386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.618151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5051528
X-RAY DIFFRACTIONr_chiral_restr0.0980.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216348
X-RAY DIFFRACTIONr_mcbond_it0.5741.54781
X-RAY DIFFRACTIONr_mcangle_it1.14127791
X-RAY DIFFRACTIONr_scbond_it2.04233236
X-RAY DIFFRACTIONr_scangle_it3.2464.53111
LS refinement shellResolution: 1.79→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 324 -
Rwork0.242 5798 -
obs-5798 94.58 %
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)
11.3892-0.143-0.30461.32260.02931.4865-0.0111-0.33140.08270.1776-0.0034-0.23-0.07840.37320.01450.0936-0.0507-0.08740.17480.00160.1102-17.75322.311-26.687
21.02180.2654-0.12861.12950.00070.9439-0.0110.0977-0.109-0.06590.0095-0.2405-0.00490.20270.00150.0148-0.0040.02480.07880.02260.1285-15.6138.504-55.008
30.735-0.10220.16981.1750.22220.9828-0.0063-0.15780.05240.1399-0.06170.2166-0.0013-0.09620.06810.0878-0.02770.0150.0679-0.01480.0535-47.92520.337-28.404
40.951-0.21010.12471.1708-0.16870.89470.04570.0612-0.1052-0.1063-0.03730.13360.0879-0.0513-0.00850.0615-0.0207-0.0350.02590.00980.0507-46.2083.2-54.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION1A225
3X-RAY DIFFRACTION1A226 - 743
4X-RAY DIFFRACTION2B2 - 217
5X-RAY DIFFRACTION2B225 - 228
6X-RAY DIFFRACTION2B64 - 744
7X-RAY DIFFRACTION3C2 - 217
8X-RAY DIFFRACTION3C225 - 226
9X-RAY DIFFRACTION3C63 - 739
10X-RAY DIFFRACTION4D-8 - 218
11X-RAY DIFFRACTION4D225 - 227
12X-RAY DIFFRACTION4D228 - 740

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