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- PDB-4gw9: Structure of a bacteriophytochrome and light-stimulated protomer ... -

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Basic information

Entry
Database: PDB / ID: 4gw9
TitleStructure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor
Componentsbacteriophytochrome
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR / PAS/PAC SENSOR / BACTERIOPBHYTOCHROME / BACTERIOPHYTOCHROME PHOTOSENSORY AND C-TERMINAL OUTPUT TRANSDUCING DOMAINS / GENE REPRESSOR RPPPSR2 / photosensory core domain and PAS/PAC domain / Light signaling / PpsR2
Function / homology
Function and homology information


detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
PHY domain / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. ...PHY domain / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Putative PAS/PAC sensor protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsBellini, D. / Papiz, M.Z.
CitationJournal: Structure / Year: 2012
Title: Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor.
Authors: Bellini, D. / Papiz, M.Z.
History
DepositionSep 1, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionSep 26, 2012ID: 4EHO
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: bacteriophytochrome
B: bacteriophytochrome
C: bacteriophytochrome
D: bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,1638
Polymers291,8334
Non-polymers2,3314
Water5,711317
1
A: bacteriophytochrome
D: bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0824
Polymers145,9162
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-67 kcal/mol
Surface area58160 Å2
MethodPISA
2
B: bacteriophytochrome
C: bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0824
Polymers145,9162
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-67 kcal/mol
Surface area58310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.940, 146.870, 139.550
Angle α, β, γ (deg.)90.00, 101.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.686415, -0.647729, 0.330578), (-0.644982, -0.752237, -0.134676), (0.335907, -0.120773, -0.93412)95.86872, 41.39622, 113.46818
3given(-0.847618, 0.16746, -0.503489), (0.064345, -0.909449, -0.410806), (-0.526692, -0.380604, 0.76009)95.69354, 78.86018, -8.64279
4given(-0.817229, 0.55774, 0.145134), (0.535876, 0.642727, 0.547485), (0.212073, 0.525194, -0.824134)135.63954, -60.45369, 44.52623

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Components

#1: Protein
bacteriophytochrome


Mass: 72958.180 Da / Num. of mol.: 4 / Fragment: N-terminal 70 kDa fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA1537 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B3Q7C0, histidine kinase
#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FULL LENGTH PROTEIN WITH N-HIS6TAG-(1-730) WAS EXPRESSED. HOWEVER, RESIDUES 636-730 WERE LOST ...THE FULL LENGTH PROTEIN WITH N-HIS6TAG-(1-730) WAS EXPRESSED. HOWEVER, RESIDUES 636-730 WERE LOST DURING PURIFICATION/CRYSTALLIZATION. SEQUENCE CORRESPONDS TO EMBL DATABASE ACCESSION NUMBER ENA|CAE26979|CAE26979.1
Source detailsTHE PROTEIN SOURCE IS RHODOPSEUDOMONAS PALUSTRIS, STRAIN CGA009 AND THE GENE IS RPA1537. THIS GENE ...THE PROTEIN SOURCE IS RHODOPSEUDOMONAS PALUSTRIS, STRAIN CGA009 AND THE GENE IS RPA1537. THIS GENE IS FRAME SHIFTED WHICH WAS REPAIRED AND THEN NEAREST SIMILAR UNIPROT SEQUENCE IS B3Q7C0 IN STRAIN TIE-1.

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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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PROTEIN CONCENTRATION 20 MG/ML, 4% POLY-GAMMA-GLUTAMIC ACID POLYMER, 100 MM TRISHCL PH 8, 0.4 M NIACINAMIDE, 200 MM KBR, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.97911, 0.97949, 0.98244, 0.9700
2
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNEL DOUBLE MONOCHROMATORMADMx-ray1
2SI 111 CHANNEL DOUBLE MONOCHROMATORSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979491
30.982441
40.971
ReflectionResolution: 2.8→74 Å / Num. obs: 97789 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.63 / % possible all: 96.4

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Processing

Software
NameVersionClassification
GDAdata collection
SHARPphasing
REFMAC5.6.0117refinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 29.769 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 1.253 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24318 4419 5 %RANDOM
Rwork0.19952 ---
obs0.20169 83799 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.01 Å2
Baniso -1Baniso -2Baniso -3
1--2.76 Å20 Å20.46 Å2
2--11.54 Å20 Å2
3----8.59 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19306 0 172 317 19795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01919961
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213646
X-RAY DIFFRACTIONr_angle_refined_deg2.5231.98327168
X-RAY DIFFRACTIONr_angle_other_deg1.323332953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83552491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64622.659929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56153035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.75615218
X-RAY DIFFRACTIONr_chiral_restr0.1340.23022
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122497
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024257
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 308 -
Rwork0.353 5852 -
obs--98.12 %
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)
10.2668-0.08390.3591.2071-1.28312.49780.1758-0.0409-0.0532-0.053-0.11060.2354-0.06560.0592-0.06520.3650.02090.06150.0409-0.00320.516973.52938.7924.625
21.73050.3084-2.10390.3175-0.21722.81740.06340.124-0.1536-0.0643-0.11140.0093-0.0216-0.08720.0480.34150.0971-0.01380.316-0.03590.4083-50.04529.63394.736
31.8004-0.3621-1.8840.09090.46832.85220.1475-0.43540.2309-0.00510.0651-0.0694-0.33150.3783-0.21260.488-0.08080.06450.1287-0.03890.45749.31527.74537.528
40.05140.01860.44510.138-0.00734.33620.05580.007-0.0376-0.00240.07050.00050.50260.1915-0.12620.41640.00630.00020.41450.00750.366694.9938.09277.925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 635
2X-RAY DIFFRACTION1A900
3X-RAY DIFFRACTION2B8 - 634
4X-RAY DIFFRACTION2B900
5X-RAY DIFFRACTION3C8 - 633
6X-RAY DIFFRACTION3C900
7X-RAY DIFFRACTION4D8 - 635
8X-RAY DIFFRACTION4D900

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