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- PDB-5m82: Three-dimensional structure of the photoproduct state of GAF3 fro... -

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Basic information

Entry
Database: PDB / ID: 5m82
TitleThree-dimensional structure of the photoproduct state of GAF3 from Slr1393 of Synechocystis sp. PCC6803
ComponentsSensory transduction histidine kinase
KeywordsTRANSFERASE / Cyanobacteriochrome / Phycocyanobilin chromophore / Photochromicity / bilin-binding GAF domain
Function / homology
Function and homology information


phosphorelay signal transduction system / phosphorelay sensor kinase activity / histidine kinase / plasma membrane
Similarity search - Function
: / PAS domain / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...: / PAS domain / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 / PAS repeat profile. / 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
Chem-3CX / PHYCOCYANOBILIN / histidine kinase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsXu, X.-L. / Zhao, K.-H. / Gaertner, W. / Hoeppner, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural elements regulating the photochromicity in a cyanobacteriochrome
Authors: Xu, X.-L. / Hoeppner, A. / Wiebeler, C. / Zhao, K.-H. / Schapiro, I. / Gaertner, W.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_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_type.id
Revision 1.3Nov 13, 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: Sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7526
Polymers24,8571
Non-polymers8955
Water1,20767
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-57 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.286, 75.286, 71.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Sensory transduction histidine kinase


Mass: 24856.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: slr1393 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73184
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO4S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1 M NaCl, 0.1 M CAPSO pH 9.5, 0.175 M LiSO4, 14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.86→65.2 Å / Num. obs: 18191 / % possible obs: 94.4 % / Redundancy: 3.89 % / CC1/2: 1 / Rsym value: 0.027 / Net I/σ(I): 25.79
Reflection shellResolution: 1.86→1.98 Å / Redundancy: 3.07 % / Mean I/σ(I) obs: 3.37 / CC1/2: 0.92 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M85

5m85


Resolution: 1.86→65.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.398 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22872 921 5.1 %RANDOM
Rwork0.1941 ---
obs0.19596 17263 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 1.86→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 61 67 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191405
X-RAY DIFFRACTIONr_bond_other_d0.0050.021289
X-RAY DIFFRACTIONr_angle_refined_deg2.3761.9631914
X-RAY DIFFRACTIONr_angle_other_deg1.483.0012933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76723.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79815211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8571512
X-RAY DIFFRACTIONr_chiral_restr0.1440.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021627
X-RAY DIFFRACTIONr_gen_planes_other0.020.02379
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_it3.4923.532633
X-RAY DIFFRACTIONr_mcbond_other3.493.523632
X-RAY DIFFRACTIONr_mcangle_it4.3945.272790
X-RAY DIFFRACTIONr_mcangle_other4.3935.282791
X-RAY DIFFRACTIONr_scbond_it4.4143.993772
X-RAY DIFFRACTIONr_scbond_other4.4113.992773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5445.8251124
X-RAY DIFFRACTIONr_long_range_B_refined8.0329.1041650
X-RAY DIFFRACTIONr_long_range_B_other8.05529.061633
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.864→1.912 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 35 -
Rwork0.332 788 -
obs--58.24 %

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