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- PDB-3s7n: Crystal Structure of the alternate His 207 conformation of the In... -

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Basic information

Entry
Database: PDB / ID: 3s7n
TitleCrystal Structure of the alternate His 207 conformation of the Infrared Fluorescent D207H variant of Deinococcus Bacteriophytochrome chromophore binding domain at 2.45 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 / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator 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 / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase-related protein, C-terminal ...: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsAuldridge, M.E. / Satyshur, K.A. / Forest, K.T.
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
Revision 1.3Oct 9, 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: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7622
Polymers37,1761
Non-polymers5861
Water2,936163
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 area5170 Å2
ΔGint-63 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.413, 52.808, 74.801
Angle α, β, γ (deg.)90.00, 113.13, 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 binding 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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% v/v PEG 4000, 20% v/v isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 10, 2010 / Details: Mirrors
RadiationMonochromator: Montel 200 Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 12893 / Num. obs: 11526 / % possible obs: 89.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.45 / Num. unique all: 246 / % possible all: 37.5

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Processing

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

2o9c


Resolution: 2.451→30.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 19.147 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.978 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23644 623 5.4 %RANDOM
Rwork0.17423 ---
all0.17772 11553 --
obs0.17772 10904 89.37 %-
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: 47.085 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å21.9 Å2
2---0.47 Å20 Å2
3---1.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.294 Å
Refinement stepCycle: LAST / Resolution: 2.451→30.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 43 163 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222488
X-RAY DIFFRACTIONr_bond_other_d0.0010.021654
X-RAY DIFFRACTIONr_angle_refined_deg1.24523409
X-RAY DIFFRACTIONr_angle_other_deg0.8533.0024009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11723.1100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9011519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
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_it0.8761.51568
X-RAY DIFFRACTIONr_mcbond_other0.0781.5623
X-RAY DIFFRACTIONr_mcangle_it1.61622524
X-RAY DIFFRACTIONr_scbond_it1.2843920
X-RAY DIFFRACTIONr_scangle_it2.3484.5885
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.451→2.583 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 47 -
Rwork0.248 367 -
obs--49.76 %
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)
14.4438-2.6932-2.06515.92341.92719.6953-0.0116-0.1831-0.84290.9038-0.3430.40421.05850.09560.35450.2934-0.063-0.00130.12920.04720.152717.137-31.18632.35
22.1837-0.72740.04692.20230.02732.66250.1091-0.44760.02310.2342-0.23580.2021-0.0708-0.28730.12670.1254-0.07230.04120.1981-0.0770.05045.91-15.99327.119
3-1.0371-4.4854-5.73668.8347-0.68350.16161.10990.41750.71640.9049-0.75580.753-1.636-0.2788-0.35410.48040.17520.01060.2125-0.3460.4595-2.816-5.01125.208
45.62651.5567-0.5018.0123-1.47236.12760.26310.11360.2441-0.8058-0.38490.88930.4957-1.20450.12180.0844-0.0264-0.0680.3355-0.18250.1812-4.789-15.62216.575
50.910.66361.45022.49913.24542.9996-0.0864-0.10720.5165-0.4892-0.25090.2165-0.4783-0.24030.33730.10050.06050.00090.14590.01710.2892.317-13.86311.596
62.30031.0524-0.26873.13080.51352.8289-0.00450.3510.1228-0.15320.04450.3259-0.0272-0.094-0.03990.06570.0154-0.04340.08630.00740.080112.6-29.273-4.452
70.54810.2366-0.02471.59030.62081.36740.0169-0.1103-0.06210.1191-0.0333-0.05850.08660.10690.01640.0664-0.0008-0.00640.07160.00380.072119.039-29.14911.199
83.3326-0.7736-1.79220.97611.01544.8831-0.0048-0.1999-0.10120.3-0.09050.01270.2525-0.13670.09530.1284-0.05440.00710.076-0.03040.057113.722-21.37424.719
91.52421.47120.46564.4715-0.48121.01450.0099-0.09880.02210.122-0.01770.20360.0001-0.04420.00780.07930.00570.01650.0538-0.01780.069815.158-26.4738.976
103.87346.77873.989925.36495.44433.7589-0.05170.1626-0.20130.24550.43430.5065-0.0260.068-0.38260.0190.0033-0.01180.13650.01110.16065.577-29.4342.876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 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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