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- PDB-4e04: RpBphP2 chromophore-binding domain crystallized by homologue-dire... -

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Basic information

Entry
Database: PDB / ID: 40000
TitleRpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.
ComponentsBacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
KeywordsSIGNALING PROTEIN / Bacteriophytochrome chromophore binding domain / two component regulator / Response regulator RPA3017 / phosphorylation / phosphotransfer / TRANSFERASE
Function / homology
Function and homology information


detection of visible light / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription
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 / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) 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 / 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 / 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
Chem-LBV / histidine kinase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBellini, D. / Papiz, M.Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.
Authors: Bellini, D. / Papiz, M.Z.
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
B: Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5464
Polymers72,3742
Non-polymers1,1712
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-50 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.350, 79.860, 149.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1


Mass: 36187.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: phyB1, phyB2, RPA3015, RPA3016 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6N5G3
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H37N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS IN THE PDB FILE ARE AS DEFINED IN THE SEQADV RECORDS. NOTE THAT THERE IS AN INSERTED ...MUTATIONS IN THE PDB FILE ARE AS DEFINED IN THE SEQADV RECORDS. NOTE THAT THERE IS AN INSERTED RESIDUE ASN105 WHICH RESULTS IN THE SEQUENCE FOLLOWING THIS RESIDUE NUMBERED +1 MORE COMPARED TO THE NATIVE SEQUENCE (UNP Q6N5G3). IN THE MANUSCRIPT THE NATIVE SEQUENCE NUMBERING, AFTER RESIDUES 105, IS RETAINED FOR CLEARER DISCUSSIONS WHEN COMPARING ALIGNED SEQUENCES USING CLUSTALW. THEREFORE IN THE DEPOSITED PDB RESIDUES GLY106 SER107... CORRESPOND TO GLY105 SER106... IN THE MANUSCRIPT.

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growpH: 8.5
Details: 18% PEG3350, 0.2 mM MgCl2 or 0.2 mM CaCl2 and 0.1 Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→74.8 Å / Num. obs: 59311 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.023 / Net I/σ(I): 24.9
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.537 / % possible all: 99.5

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.672 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3027 5.1 %RANDOM
Rwork0.181 ---
obs0.184 56814 99.7 %-
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: 50.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.69 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.79→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 86 515 5387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3591.9826887
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60622.542236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67315790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.431557
X-RAY DIFFRACTIONr_chiral_restr0.1470.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213953
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021021
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_it1.2591.53017
X-RAY DIFFRACTIONr_mcbond_other0.3861.51205
X-RAY DIFFRACTIONr_mcangle_it2.15324863
X-RAY DIFFRACTIONr_scbond_it3.13531852
X-RAY DIFFRACTIONr_scangle_it4.8934.51772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 180 -
Rwork0.262 3839 -
obs--99.38 %
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)
11.2337-0.7346-0.50642.04550.151.2759-0.0123-0.1834-0.06620.3690.0671-0.01650.00810.0172-0.05490.1126-0.0054-0.04330.07060.00570.040822.33023.713365.4438
20.57980.0579-0.27091.31690.30121.3709-0.0099-0.00040.0184-0.0488-0.08010.2319-0.0361-0.18840.090.01040.0064-0.00530.0512-0.0130.087414.3269-17.338739.0999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 320
2X-RAY DIFFRACTION1A400
3X-RAY DIFFRACTION1A501 - 777
4X-RAY DIFFRACTION2B11 - 320
5X-RAY DIFFRACTION2B400
6X-RAY DIFFRACTION2B501 - 738

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