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- PDB-3zq5: Structure of the Y263F mutant of the cyanobacterial phytochrome Cph1 -

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Basic information

Entry
Database: PDB / ID: 3zq5
TitleStructure of the Y263F mutant of the cyanobacterial phytochrome Cph1
ComponentsPHYTOCHROME-LIKE PROTEIN CPH1
KeywordsTRANSFERASE / ARGININE FINGER / TANDEM GAF DOMAIN / 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
ACETATE ION / PHYCOCYANOBILIN / PHOSPHATE ION / Phytochrome-like protein Cph1
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMailliet, J. / Psakis, G. / Sineshchekov, V. / Essen, L.-O. / Hughes, J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Spectroscopy and a High-Resolution Crystal Structure of Tyr263 Mutants of Cyanobacterial Phytochrome Cph1.
Authors: Mailliet, J. / Psakis, G. / Feilke, K. / Sineshchekov, V. / Essen, L.-O. / Hughes, J.
History
DepositionJun 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)59,89911
Polymers58,7491
Non-polymers1,15010
Water5,909328
1
A: PHYTOCHROME-LIKE PROTEIN CPH1
hetero molecules

A: PHYTOCHROME-LIKE PROTEIN CPH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,79922
Polymers117,4992
Non-polymers2,30020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11960 Å2
ΔGint-108.7 kcal/mol
Surface area44890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.570, 95.150, 73.580
Angle α, β, γ (deg.)90.00, 99.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHYTOCHROME-LIKE PROTEIN CPH1 / LIGHT-REGULATED HISTIDINE KINASE 1 / BACTERIOPHYTOCHROME CPH1


Mass: 58749.488 Da / Num. of mol.: 1 / Fragment: SENSORY MODULE, RESIDUES 1-514 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. PCC 6803 (bacteria) / Production host: Escherichia coli DH5[alpha] (bacteria) / Variant (production host): P45.2 / References: UniProt: Q55168, histidine kinase

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Non-polymers , 6 types, 338 molecules

#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 263 TO PHE
Has protein modificationY
Nonpolymer detailsPHYCOCYANOBILIN (CYC): CHROMOPHORE

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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: 3.16 Å3/Da / Density % sol: 61.07 % / Description: NONE
Crystal growpH: 7.2
Details: 10 MG / ML PROTEIN, 1.9 M SODIUM ACETATE, 0.4 M MES PH 7.2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.94→33.9 Å / Num. obs: 53522 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.37 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.4 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEA

2vea


Resolution: 1.95→33.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.676 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21765 2662 5 %RANDOM
Rwork0.17364 ---
obs0.17578 50593 99.32 %-
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: 50.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.72 Å2
2--1.32 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 78 328 4508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224324
X-RAY DIFFRACTIONr_bond_other_d0.0010.022870
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9675892
X-RAY DIFFRACTIONr_angle_other_deg0.8913.0016994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3435534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95223.942208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68515704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6261530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214837
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02881
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_it1.2961.52620
X-RAY DIFFRACTIONr_mcbond_other0.3561.51045
X-RAY DIFFRACTIONr_mcangle_it2.34124240
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.30531704
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2524.51643
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: 1.945→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 179 -
Rwork0.296 3472 -
obs--92.31 %
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)
14.8933-1.8731.57774.5508-6.535512.5850.21290.3878-0.6106-0.94170.09690.22221.6251-0.5744-0.30980.5507-0.0361-0.09510.1846-0.12150.5086.1116-19.08859.603
22.255-0.61171.80992.6244-0.29452.1744-0.1054-0.33820.02210.26490.0915-0.1775-0.0075-0.20180.01390.12450.09240.01120.1168-0.00210.120525.3167-13.679838.4475
31.2535-0.2185-0.22121.44920.27951.5668-0.03580.04970.0462-0.1337-0.0222-0.05230.0210.04030.0580.02960.0056-0.00150.00580.00520.02138.99673.936124.5912
41.9817-0.0368-0.19961.03750.15082.9178-0.13450.1982-0.2007-0.05710.00950.21350.257-0.20270.1250.0770.01460.00740.09540.00350.1088-31.48617.446814.1661
54.0751-3.17931.25113.2832-1.21091.12150.12870.1331-0.1527-0.0908-0.1321-0.07790.3445-0.00150.00340.17970.0307-0.00310.1811-0.0240.07024.4526-5.12235.0647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 18
2X-RAY DIFFRACTION2A19 - 125
3X-RAY DIFFRACTION2A230 - 252
4X-RAY DIFFRACTION3A132 - 229
5X-RAY DIFFRACTION3A253 - 321
6X-RAY DIFFRACTION4A322 - 442
7X-RAY DIFFRACTION4A485 - 514
8X-RAY DIFFRACTION5A444 - 484

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