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- PDB-1ztu: Structure of the chromophore binding domain of bacterial phytochrome -

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Basic information

Entry
Database: PDB / ID: 1ztu
TitleStructure of the chromophore binding domain of bacterial phytochrome
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIVERDIN IX / CHROMOPHORE / PAS / GAF / KNOT
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain ...Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
BILIVERDINE IX ALPHA / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsWagner, J.R. / Brunzelle, J.S. / Forest, K.T. / Vierstra, R.D.
CitationJournal: Nature / Year: 2005
Title: A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.
Authors: Wagner, J.R. / Brunzelle, J.S. / Forest, K.T. / Vierstra, R.D.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9962
Polymers37,4131
Non-polymers5831
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.876, 133.666, 49.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37413.223 Da / Num. of mol.: 1 / Fragment: Chromophore Bindidng Domain / Mutation: P240T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: bphP / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834pLysS
References: UniProt: Q9RZA4, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.244 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.95
Details: PEG 400, sodium acetate, pH 4.95, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1981
2981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 32-ID10.9793, 0.9791
SYNCHROTRONAPS 32-ID20.9793, 0.9791
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 25, 2004
MARRESEARCH2CCDOct 25, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond 111MADMx-ray1
2Diamond 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
ReflectionResolution: 2.5→30 Å / Num. obs: 15209 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 10.8 / % possible all: 90.4

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.5 Å / D res low: 19.87 Å / FOM acentric: 0.404 / FOM centric: 0.135 / Reflection acentric: 12722 / Reflection centric: 2038
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
9.81-19.870.7070.341159106
7.4-9.810.6720.23626299
6.19-7.40.6360.209340109
5.43-6.190.6630.179404106
4.89-5.430.6250.174467101
4.49-4.890.5820.183502100
4.17-4.490.5330.15256496
3.91-4.170.5190.153599104
3.7-3.910.4980.133665108
3.51-3.70.4720.144662103
3.35-3.510.4520.117720100
3.21-3.350.4280.136752117
3.09-3.210.4080.141772100
2.98-3.090.3730.133795105
2.88-2.980.3740.117811104
2.79-2.880.3290.113829102
2.71-2.790.231084094
2.64-2.710.2020854102
2.57-2.640.191086192
2.5-2.570.183086490

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 29.116 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.283
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26569 751 5 %RANDOM
Rwork0.23746 ---
obs0.23887 14403 97.08 %-
all-15154 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.759 Å2
Baniso -1Baniso -2Baniso -3
1--7.09 Å20 Å20 Å2
2---8.42 Å20 Å2
3---15.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 43 34 2485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9943451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56222.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54515371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5511519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021938
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21679
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3760.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4291.51606
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76722528
X-RAY DIFFRACTIONr_scbond_it1.15331205
X-RAY DIFFRACTIONr_scangle_it1.9444.5923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 49 -
Rwork0.39 955 -
obs--90.04 %

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