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- PDB-4bwi: Structure of the phytochrome Cph2 from Synechocystis sp. PCC6803 -

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Basic information

Entry
Database: PDB / ID: 4bwi
TitleStructure of the phytochrome Cph2 from Synechocystis sp. PCC6803
ComponentsPHYTOCHROME-LIKE PROTEIN CPH2
KeywordsTRANSFERASE / PHYCOCYANOBILIN / PCB / RED LIGHT PHOTORECEPTOR
Function / homology
Function and homology information


red or far-red light photoreceptor activity / red, far-red light phototransduction / cyclic-guanylate-specific phosphodiesterase activity / detection of visible light / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / Phytochrome / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome region ...: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / Phytochrome / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / FORMIC ACID / GLUTAMIC ACID / Phytochrome-like protein cph2
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsAnders, K. / Angerer, V. / Widany, G.D. / Mroginski, M.A. / von Stetten, D. / Essen, L.-O.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Cyanobacterial Phytochrome 2 Photosensor Implies a Tryptophan Switch for Phytochrome Signaling.
Authors: Anders, K. / Daminelli-Widany, G. / Mroginski, M.A. / von Stetten, D. / Essen, L.-O.
History
DepositionJul 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 13, 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 / reflns / reflns_shell / 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 / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHYTOCHROME-LIKE PROTEIN CPH2
B: PHYTOCHROME-LIKE PROTEIN CPH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28214
Polymers98,4512
Non-polymers1,83112
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-58.2 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.430, 88.460, 84.870
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHYTOCHROME-LIKE PROTEIN CPH2 / BACTERIOPHYTOCHROME CPH2


Mass: 49225.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THIOETHER LINK BETWEEN C129 AND CYC / Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC6803 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q55434

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Non-polymers , 5 types, 193 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.23 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: (20 MG/ML SYNCPH2(1-2) IN PR IN 10 MM HEPES, 100 MM NACL, PH 8.0); (0.1 M HEPES PH 7.0, 1.0 M NH4COOH, 0.1% (W/V) LYSINE, 0.16% (W/V) ARGININE, 0.05% (W/V) GLUTAMATE); STREAK SEEDING, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→46.5 Å / Num. obs: 32838 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 50.91 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.4 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→29.632 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1624 5 %
Rwork0.2 --
obs0.2026 32757 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 129 181 6305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026260
X-RAY DIFFRACTIONf_angle_d0.6228501
X-RAY DIFFRACTIONf_dihedral_angle_d13.3822288
X-RAY DIFFRACTIONf_chiral_restr0.041934
X-RAY DIFFRACTIONf_plane_restr0.0021087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67650.40011370.29282597X-RAY DIFFRACTION98
2.6765-2.76280.37531340.26682573X-RAY DIFFRACTION98
2.7628-2.86150.30791450.24512578X-RAY DIFFRACTION100
2.8615-2.97590.36421120.24752648X-RAY DIFFRACTION100
2.9759-3.11120.3181190.23312629X-RAY DIFFRACTION100
3.1112-3.27510.29271390.23132645X-RAY DIFFRACTION100
3.2751-3.480.25571780.22372521X-RAY DIFFRACTION98
3.48-3.74820.3309850.23222516X-RAY DIFFRACTION94
3.7482-4.12450.23071610.19752431X-RAY DIFFRACTION93
4.1245-4.71920.18181550.15132637X-RAY DIFFRACTION100
4.7192-5.93780.23471300.16352656X-RAY DIFFRACTION100
5.9378-29.63420.21221290.1722702X-RAY DIFFRACTION100
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)
16.1780.87880.64422.97030.50172.9686-0.05060.4198-0.2501-0.18830.1032-0.18820.09050.1034-0.02810.22870.00980.01480.3401-0.02380.29081.9809-26.7524-15.1667
22.46710.73151.03571.40161.13111.98280.08910.53590.0257-0.05660.2195-0.1647-0.06940.3907-0.37210.27040.06260.02030.25670.05390.370421.4549-16.4664-5.7207
34.25962.0779-1.29326.1914-2.10113.61290.3279-0.3812-0.57080.9372-0.34410.32070.20960.1262-0.0390.5292-0.093-0.02510.3883-0.0370.51125.9679-16.527927.1236
43.05581.19342.12867.3586-1.63816.80850.3745-0.0675-0.03570.362-0.1166-0.38730.3552-0.2507-0.09770.3269-0.0908-0.00050.2807-0.02630.241624.4004-18.649123.1028
55.37070.292.92065.797-0.69178.0011-0.18320.9748-0.5046-0.3974-0.1988-0.77940.54761.069-0.36760.3750.07450.1090.3057-0.1050.461934.869-16.180615.1331
62.7851-2.2146-0.47181.8757-0.60198.2193-1.08790.21821.46760.01760.135-0.1766-0.7313-1.58830.87760.56030.1615-0.03220.85310.19481.046215.8049-12.2283-27.244
75.0015-0.30791.45352.64240.18983.12990.31120.92370.2422-0.5699-0.18450.29770.0447-0.05580.06090.38220.1123-0.04230.5250.00170.346823.2542-19.7203-26.4321
81.69930.74560.30692.94780.09183.23410.28391.3866-1.4953-0.72070.0779-0.12430.123-0.8151-0.26260.9293-0.1763-0.11261.5121-0.41591.002422.6558-35.5579-54.2838
90.6555-0.51040.56575.59060.67010.7201-0.17420.8225-0.5861-1.50350.25740.07940.3565-0.6025-0.23981.0346-0.4887-0.06041.1739-0.31640.723923.3121-36.0458-49.9604
106.8955-0.27363.57390.0427-0.5563.68240.09280.9947-0.621-0.46550.0014-0.04810.56710.4129-0.11710.5774-0.05570.05770.4895-0.1070.476548.8033-32.8295-31.6871
115.11183.97226.48254.56513.93339.2154-0.70420.68512.17760.0690.3842-0.1305-0.65291.2620.35130.6875-0.03860.11120.6838-0.12150.938332.6961-7.6035-7.4131
128.68753.09046.17141.25282.30734.4250.2854-1.206-0.44220.3045-0.3101-0.2256-0.279-0.8403-0.01060.543-0.0861-0.04550.6751-0.07010.5258-0.1851-23.25875.6861
133.8142-0.65910.22033.33610.11533.00110.0009-0.52770.20070.2280.08160.0372-0.05550.1176-0.06680.2234-0.01320.02480.2815-0.05680.232845.4716-26.111-12.319
141.7791-2.00670.36863.2642-1.76221.89330.48911.2233-0.4820.02520.110.8749-0.33-0.5422-0.65290.74640.1030.11461.40990.00240.660114.4526-30.497-42.985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 23:168)
2X-RAY DIFFRACTION2CHAIN A AND ((RESID 169:216) OR RESID 501)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 217:331)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 332:361)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 401:421)
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 6:22)
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 169:216)
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 217:331)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 332:361)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 362:400)
11X-RAY DIFFRACTION11CHAIN A AND (RESID 4:22)
12X-RAY DIFFRACTION12CHAIN A AND (RESID 362:400)
13X-RAY DIFFRACTION13CHAIN B AND ((RESID 23:168) OR RESID 501)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 401:418)

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