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- PDB-5akp: Crystal structure of the dark-adapted full-length bacteriophytoch... -

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Basic information

Entry
Database: PDB / ID: 5akp
TitleCrystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore
ComponentsPHYTOCHROME-LIKE PROTEIN
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR / BACTERIAL PROTEIN / PHOTOSENSOR / RED/FAR-RED LIGHT / PHYTOCHROME / PROTEIN STRUCTURE / SIGNAL TRANSDUCTION / XANTHOMONAS / PHYTOPATHOGEN
Function / homology
Function and homology information


: / : / detection of visible light / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
: / PAS fold / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain ...: / PAS fold / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / PAS domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Bacteriophytochrome / Bacteriophytochrome
Similarity search - Component
Biological speciesXANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsOtero, L.H. / Klinke, S. / Goldbaum, F.A. / Bonomi, H.R.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas Campestris Provides Clues to its Long-Range Signaling Mechanism.
Authors: Otero, L.H. / Klinke, S. / Rinaldi, J. / Velazquez-Escobar, F. / Mroginski, M.A. / Lopez, M.F. / Malamud, F. / Vojnov, A.A. / Hildebrandt, P. / Goldbaum, F.A. / Bonomi, H.R.
History
DepositionMar 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHYTOCHROME-LIKE PROTEIN
B: PHYTOCHROME-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9777
Polymers142,5322
Non-polymers1,4455
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-60.9 kcal/mol
Surface area52730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.942, 103.942, 344.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PHYTOCHROME-LIKE PROTEIN / XCCBPHP


Mass: 71266.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THIOETHER BOND BETWEEN THE A-RING CBC SIDE CHAIN FROM BV AND THE CYS 13
Source: (gene. exp.) XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
Strain: 8004 / Plasmid: PET-24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q4UNU4, UniProt: A0A0H2XCS3*PLUS
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.27 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 8.3
Details: 12%(W/V) PEG 4000, 0.1 M TRIS, 0.2 M SODIUM ACETATE PH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2013 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.25→47.35 Å / Num. obs: 30865 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 94.46 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.6
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GW9

4gw9


Resolution: 3.25→41.75 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.453
Details: 11 N-TERMINAL RESIDUES AND RESIDUES FROM 456 TO 470 NOT MODELED, WEAK ELECTRON DENSITY IS SHOWN AT THE AREA WHERE THE D-RING FROM BV CHROMOPHORE IS PLACED.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1497 4.87 %RANDOM
Rwork0.2028 ---
obs0.2053 30757 99.91 %-
Displacement parametersBiso mean: 114.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.1889 Å20 Å20 Å2
2--2.1889 Å20 Å2
3----4.3778 Å2
Refine analyzeLuzzati coordinate error obs: 0.846 Å
Refinement stepCycle: LAST / Resolution: 3.25→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9390 0 103 2 9495
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019711HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1913251HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4458SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes227HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1494HARMONIC5
X-RAY DIFFRACTIONt_it9711HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion4.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1247SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11501SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.36 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3741 136 4.62 %
Rwork0.288 2805 -
all0.2918 2941 -
obs--99.91 %
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)
10.56820.4-0.09881.4224-0.97962.40250.0655-0.15160.09270.0541-0.1358-0.2806-0.33990.54420.0703-0.2857-0.1520.0591-0.304-0.0661-0.016830.480166.0339-6.4001
21.04210.3395-0.98241.1841-0.62822.39980.1269-0.07580.21370.18080.02240.2717-0.2255-0.3837-0.1492-0.2487-0.11220.055-0.2727-0.1242-0.00566.963266.2511-8.7116

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