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- PDB-2vea: The complete sensory module of the cyanobacterial phytochrome Cph... -

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Basic information

Entry
Database: PDB / ID: 2vea
TitleThe complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.
ComponentsPHYTOCHROME-LIKE PROTEIN CPH1
KeywordsTRANSFERASE / ARGININE FINGER / PHOSPHORYLATION / TANDEM GAF DOMAIN / KNOT / KINASE / RECEPTOR / PAS DOMAIN / CHROMOPHORE / SENSORY TRANSDUCTION / PHOTORECEPTOR PROTEIN / BILIN-LIKE CHROMOPHORE / PHYTOCHROME / PHOTORECEPTOR
Function / homology
Function and homology information


red or far-red light photoreceptor activity / response to red or far red light / red, far-red light phototransduction / protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay sensor kinase activity / protein autophosphorylation / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
: / PHY domain / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain ...: / PHY domain / Phytochrome / 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. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / 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 / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / 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
PHYCOCYANOBILIN / Phytochrome-like protein Cph1
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsEssen, L.-O. / Mailliet, J. / Hughes, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The Structure of a Complete Phytochrome Sensory Module in the Pr Ground State.
Authors: Essen, L.-O. / Mailliet, J. / Hughes, J.
History
DepositionOct 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: PHYTOCHROME-LIKE PROTEIN CPH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3542
Polymers58,7651
Non-polymers5891
Water52229
1
A: PHYTOCHROME-LIKE PROTEIN CPH1
hetero molecules

A: PHYTOCHROME-LIKE PROTEIN CPH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7084
Polymers117,5312
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7760 Å2
ΔGint-71.3 kcal/mol
Surface area44540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.180, 77.180, 249.000
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 CPH1 / LIGHT-REGULATED HISTIDINE KINASE 1 / BACTERIOPHYTOCHROME CPH1 / CYANOBACTERIAL PHYTOCHROME CPH1


Mass: 58765.488 Da / Num. of mol.: 1 / Fragment: SENSORY MODULE, RESIDUES 1-514
Source method: isolated from a genetically manipulated source
Details: THIOETHER LINKAGE BETWEEN C259 AND C3(1) ATOM OF PHYCOCYANOBILIN CHROMOPHORE
Source: (gene. exp.) SYNECHOCYSTIS SP. PCC 6803 (bacteria) / Plasmid: P926.5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / Variant (production host): P45.2 / References: UniProt: Q55168
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPHYCOCYANOBILIN (CYC): RING D IS TILTED BY 23 DEGREE RELATIVE TO COPLANAR RINGS B AND C
Sequence detailsTRANSMITTER REGION L515-N748 REPLACED BY HEXAHISTIDINE TAG

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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: 3.2 Å3/Da / Density % sol: 55.5 %
Description: DUE TO STRONG ANISOTROPISM OF THE CRYSTALS, DIFFRACTION DATA WERE RESCALED USING THE DIFFRACTION ANISOTROPY SERVER. THE FOLLOWING ANISOTROPIC CORRECTION WAS APPLIED TO THE NATIVE ...Description: DUE TO STRONG ANISOTROPISM OF THE CRYSTALS, DIFFRACTION DATA WERE RESCALED USING THE DIFFRACTION ANISOTROPY SERVER. THE FOLLOWING ANISOTROPIC CORRECTION WAS APPLIED TO THE NATIVE DATASETS, VALUES GIVEN IN SQUARE- ANGSTROM, -35.88,-35.88,17.94. THE COMPLETENESS OF THE NATIVE DATASET AT 2.7 ANGSTROM RESOLUTION WAS 98.5 PERCENT
Crystal growpH: 6.7
Details: TETRAGONAL CRYSTALS OF THE CPH1 PR STATE WERE GROWN IN 96-WELL CRYSTALLIZATION PLATES USING DROPS COMPRISING 500 NL 10 MG/ML CPH1-DELTA2 IN 2.5 MM TRIS/HCL PH 7.8, 15 MM NACL PLUS 500 NL ...Details: TETRAGONAL CRYSTALS OF THE CPH1 PR STATE WERE GROWN IN 96-WELL CRYSTALLIZATION PLATES USING DROPS COMPRISING 500 NL 10 MG/ML CPH1-DELTA2 IN 2.5 MM TRIS/HCL PH 7.8, 15 MM NACL PLUS 500 NL RESERVOIR SOLUTION (2.1 M SODIUM ACETATE, PH 6.7).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 13, 2007 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 26939 / % possible obs: 67.2 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.5 / % possible all: 6.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.21→24.68 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.506 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.PHYTOCHROME CRYSTAL IS IN THE PR STATE. DISORDERED LOOP REGIONS (Q73-R80, G100-D101, R148-Q150, E463- G465) ARE NOT INCLUDED IN MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1062 4 %RANDOM
Rwork0.244 ---
obs0.245 25188 68.1 %-
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: 65.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.01 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.21→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 43 29 4006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214092
X-RAY DIFFRACTIONr_bond_other_d0.0010.022694
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9625577
X-RAY DIFFRACTIONr_angle_other_deg0.85936556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29723.717191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.741527
X-RAY DIFFRACTIONr_chiral_restr0.0620.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024557
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02841
X-RAY DIFFRACTIONr_nbd_refined0.1890.2986
X-RAY DIFFRACTIONr_nbd_other0.1820.22854
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21954
X-RAY DIFFRACTIONr_nbtor_other0.0830.22182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2551.52672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4224037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.49131737
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7584.51538
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 8
Rwork0.337 113

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