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- PDB-3s7p: Crystal Structure of the Infrared Fluorescent D207H variant of De... -

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Basic information

Entry
Database: PDB / ID: 3s7p
TitleCrystal Structure of the Infrared Fluorescent D207H variant of Deinococcus Bacteriophytochrome chromophore binding domain at 1.72 angstrom resolution
ComponentsBacteriophytochrome
KeywordsFLUORESCENT PROTEIN / BILIVERDIN / PAS / GAF / Phytochrome / bacteriophytochrome / Photoreceptor
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain ...Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.722 Å
AuthorsForest, K.T. / Auldridge, M.E. / Satyshur, K.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein.
Authors: Auldridge, M.E. / Satyshur, K.A. / Anstrom, D.M. / Forest, K.T.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7622
Polymers37,1761
Non-polymers5861
Water5,368298
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5244
Polymers74,3532
Non-polymers1,1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5030 Å2
ΔGint-55 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.072, 51.666, 80.228
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37176.418 Da / Num. of mol.: 1 / Fragment: chromophore binidng domain (UNP Residues 1-321) / Mutation: D207H Y307S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: bphP, DR_A0050 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% v/v PEG 4000, 20% v/v isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 34268 / Num. obs: 33621 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 31.12
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.53 / Num. unique all: 1642 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9C

2o9c


Resolution: 1.722→43.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.267 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19623 1701 5.1 %RANDOM
Rwork0.16753 ---
all0.16901 33564 --
obs0.16901 31863 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.053 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0.08 Å2
2--0.48 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.722→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 43 298 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222548
X-RAY DIFFRACTIONr_bond_other_d0.0010.021696
X-RAY DIFFRACTIONr_angle_refined_deg1.47923496
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0024119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79522.941102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69315383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0311520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
X-RAY DIFFRACTIONr_mcbond_it0.7421.51600
X-RAY DIFFRACTIONr_mcbond_other0.1541.5633
X-RAY DIFFRACTIONr_mcangle_it1.34322586
X-RAY DIFFRACTIONr_scbond_it2.0133948
X-RAY DIFFRACTIONr_scangle_it3.2434.5909
LS refinement shellResolution: 1.722→1.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 111 -
Rwork0.181 2167 -
obs--90.43 %
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)
11.8748-0.2525-0.91290.1780.6065.73650.0069-0.2749-0.27790.2152-0.1495-0.10860.3695-0.00950.14260.2218-0.1232-0.07450.17950.10720.143117.137-31.18632.35
21.3462-0.16140.06320.46920.30631.06120.09-0.26880.13860.0396-0.1282-0.01540.0365-0.14460.03810.1088-0.03880.01420.1677-0.04680.08838.164-18.09725.772
39.2181-4.9924-3.76865.45253.81492.03080.7908-0.36450.9942-0.7201-0.5447-0.1306-0.5716-0.3619-0.24610.21190.0809-0.00720.2605-0.17170.2005-2.816-5.01125.208
42.14931.2183-1.01153.60011.23415.71110.11460.18010.1479-0.9844-0.51130.19130.1827-0.77630.39680.40090.1230.01170.1909-0.03570.0898-4.789-15.62216.575
50.88880.41170.61450.42780.97162.1572-0.0085-0.00420.3397-0.0987-0.0850.1218-0.1748-0.15020.09360.12190.0370.00530.09730.00940.2172.317-13.86311.596
60.89420.4196-0.11861.69180.73771.1739-0.02580.12080.0089-0.0943-0.0140.1479-0.0904-0.00590.03980.10180.0143-0.01570.10510.00020.116212.6-29.273-4.452
70.40730.31110.2320.85530.61690.96480.0524-0.0354-0.04440.07330.0069-0.0650.06160.0808-0.05940.09710.0069-0.0080.09270.00730.105419.039-29.14911.199
82.9208-0.4962-1.60120.53290.4462.121-0.0048-0.1555-0.05640.1322-0.0469-0.03170.10710.00110.05180.1252-0.0284-0.00280.1155-0.00990.084513.722-21.37424.719
90.62330.67240.11392.0465-0.23760.54210.01660.01250.0020.03210.02660.05640.02890.0134-0.04310.10460.00040.00420.09410.00010.10515.158-26.4738.976
102.25352.68581.886213.6853.60031.5961-0.12550.17-0.18380.04690.23630.2219-0.07560.149-0.11080.0868-0.00410.00150.12330.00350.13645.577-29.4342.876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 23
2X-RAY DIFFRACTION2A24 - 60
3X-RAY DIFFRACTION2A330
4X-RAY DIFFRACTION3A61 - 84
5X-RAY DIFFRACTION4A85 - 105
6X-RAY DIFFRACTION5A106 - 143
7X-RAY DIFFRACTION6A144 - 170
8X-RAY DIFFRACTION7A171 - 234
9X-RAY DIFFRACTION8A235 - 267
10X-RAY DIFFRACTION9A268 - 296
11X-RAY DIFFRACTION10A297 - 323

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