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- PDB-2x9i: Structure of the Mutant D105N of Phycoerythrobilin Synthase PebS ... -

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Basic information

Entry
Database: PDB / ID: 2x9i
TitleStructure of the Mutant D105N of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in complex with bound substrate Biliverdin IXA
ComponentsPHYCOBILIN SYNTHASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


phycoerythrobilin synthase / phytochromobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding
Similarity search - Function
oxygen-dependent coproporphyrinogen oxidase - #20 / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Phycoerythrobilin synthase
Similarity search - Component
Biological speciesPROCHLOROCOCCUS PHAGE P-SSM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBusch, A.W.U. / Frankenberg-Dinkel, N. / Hofmann, E.
CitationJournal: Biochem.J. / Year: 2011
Title: Radical Mechanism of Cyanophage Phycoerythrobilin Synthase (Pebs).
Authors: Busch, A.W.U. / Reijerse, E.J. / Lubitz, W. / Hofmann, E. / Frankenberg-Dinkel, N.
History
DepositionMar 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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: PHYCOBILIN SYNTHASE
B: PHYCOBILIN SYNTHASE
C: PHYCOBILIN SYNTHASE
D: PHYCOBILIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69010
Polymers109,1674
Non-polymers2,5236
Water6,287349
1
A: PHYCOBILIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9713
Polymers27,2921
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHYCOBILIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9713
Polymers27,2921
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHYCOBILIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8752
Polymers27,2921
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PHYCOBILIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8752
Polymers27,2921
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.920, 70.140, 81.970
Angle α, β, γ (deg.)109.38, 109.25, 92.56
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
13
23
14
24
15
25
16
26
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 22:135 OR RESSEQ 148:202 OR RESSEQ 209:233 )
211CHAIN B AND (RESSEQ 22:135 OR RESSEQ 148:202 OR RESSEQ 209:233 )
311CHAIN C AND (RESSEQ 22:135 OR RESSEQ 148:202 OR RESSEQ 209:233 )
411CHAIN D AND (RESSEQ 22:135 OR RESSEQ 148:202 OR RESSEQ 209:233 )
112CHAIN A AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND BACKBONE
212CHAIN D AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND BACKBONE
113CHAIN A AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND SIDECHAIN
213CHAIN D AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND SIDECHAIN
114CHAIN B AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND BACKBONE
214CHAIN C AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND BACKBONE
115CHAIN B AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND SIDECHAIN
215CHAIN C AND (RESSEQ 21 OR RESSEQ 136:147 OR RESSEQ 203:208) AND SIDECHAIN
116CHAIN A AND (RESSEQ 1234)
216CHAIN D AND (RESSEQ 1234)
117CHAIN B AND (RESSEQ 1234)
217CHAIN C AND (RESSEQ 1234)

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper:
IDCodeMatrixVector
1given(-0.990048, 0.13402, 0.042945), (-0.129498, -0.748089, -0.650841), (-0.055099, -0.649925, 0.757999)2.17905, 45.6621, -24.8112
2given(-0.990168, -0.129089, -0.053876), (-0.133448, 0.756307, 0.640462), (-0.04193, 0.641355, -0.766098)33.5451, 39.1349, -100.356
3given(0.999976, -0.0019, 0.006642), (-0.001917, -0.999995, 0.002639), (0.006637, -0.002652, -0.999974)-25.9623, 57.7726, -52.1334

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Components

#1: Protein
PHYCOBILIN SYNTHASE / (3Z)-PHYCOERYTHROBILIN \: FERREDOXIN OXIDOREDUCTASE / BILIVERDIN REDUCTASE


Mass: 27291.857 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLOROCOCCUS PHAGE P-SSM2 (virus) / Description: CYANOPHAGE / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58MU6, phycoerythrobilin synthase
#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 105 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 105 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, ASP 105 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 105 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASP 105 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASP 105 TO ASN

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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: 2.58 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 170MM (NH4)2SO4, 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→43 Å / Num. obs: 50826 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 29.43 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.56
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.73 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGR

2vgr


Resolution: 2.2→43.01 Å / SU ML: 0.3 / σ(F): 2 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 2561 5 %
Rwork0.1764 --
obs0.1783 50817 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.74 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.5789 Å2-0.8586 Å20.9726 Å2
2--14.1141 Å27.3864 Å2
3----7.5353 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6870 0 182 349 7401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127250
X-RAY DIFFRACTIONf_angle_d1.4359808
X-RAY DIFFRACTIONf_dihedral_angle_d18.1062598
X-RAY DIFFRACTIONf_chiral_restr0.096974
X-RAY DIFFRACTIONf_plane_restr0.0071258
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1575X-RAY DIFFRACTIONPOSITIONAL
12B1575X-RAY DIFFRACTIONPOSITIONAL0.008
13C1575X-RAY DIFFRACTIONPOSITIONAL0.008
14D1575X-RAY DIFFRACTIONPOSITIONAL0.007
21A76X-RAY DIFFRACTIONPOSITIONAL
22D76X-RAY DIFFRACTIONPOSITIONAL0.004
31A83X-RAY DIFFRACTIONPOSITIONAL
32D83X-RAY DIFFRACTIONPOSITIONAL0.46
41B60X-RAY DIFFRACTIONPOSITIONAL
42C60X-RAY DIFFRACTIONPOSITIONAL0.004
51B66X-RAY DIFFRACTIONPOSITIONAL
52C66X-RAY DIFFRACTIONPOSITIONAL0.679
61A43X-RAY DIFFRACTIONPOSITIONAL
62D43X-RAY DIFFRACTIONPOSITIONAL0.003
71B43X-RAY DIFFRACTIONPOSITIONAL
72C43X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.242200.20962761X-RAY DIFFRACTION96
2.2422-2.28800.20292826X-RAY DIFFRACTION97
2.288-2.33770.25783110.19762528X-RAY DIFFRACTION97
2.3377-2.392100.18752858X-RAY DIFFRACTION97
2.3921-2.45190.23292990.18432492X-RAY DIFFRACTION97
2.4519-2.518200.18662828X-RAY DIFFRACTION97
2.5182-2.59230.25722840.18592537X-RAY DIFFRACTION97
2.5923-2.67590.22182150.18722618X-RAY DIFFRACTION97
2.6759-2.771600.18972840X-RAY DIFFRACTION97
2.7716-2.88250.23462040.19262623X-RAY DIFFRACTION97
2.8825-3.01370.24711950.20742629X-RAY DIFFRACTION97
3.0137-3.17250.25961680.20482643X-RAY DIFFRACTION96
3.1725-3.37120.26741440.19332672X-RAY DIFFRACTION97
3.3712-3.63140.18281460.17332660X-RAY DIFFRACTION97
3.6314-3.99660.16651330.14922676X-RAY DIFFRACTION96
3.9966-4.57430.14951750.12962657X-RAY DIFFRACTION97
4.5743-5.7610.17461210.13042727X-RAY DIFFRACTION98
5.761-43.01780.17911660.15832681X-RAY DIFFRACTION97

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