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- PDB-2x9j: Structure of the Mutant D206N of Phycoerythrobilin Synthase PebS ... -

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Basic information

Entry
Database: PDB / ID: 2x9j
TitleStructure of the Mutant D206N of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in complex with bound substrate Biliverdin IXA
ComponentsPHYCOERYTHROBILIN SYNTHASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


phycoerythrobilin synthase / phytochromobilin biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / 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: 1.85 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 21, 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: PHYCOERYTHROBILIN SYNTHASE
B: PHYCOERYTHROBILIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7494
Polymers54,5842
Non-polymers1,1652
Water7,728429
1
A: PHYCOERYTHROBILIN 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
2
B: PHYCOERYTHROBILIN 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)53.810, 63.150, 81.650
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESSEQ 1234
211CHAIN B AND RESSEQ 1234
112CHAIN A AND (RESSEQ 22:54 OR RESSEQ 57:63 OR RESSEQ...
212CHAIN B AND (RESSEQ 22:54 OR RESSEQ 57:63 OR RESSEQ...
113CHAIN A AND (RESSEQ 22:54 OR RESSEQ 57:63 OR RESSEQ...
213CHAIN B AND (RESSEQ 22:54 OR RESSEQ 57:63 OR RESSEQ...

NCS ensembles :
ID
1
2
3

NCS oper: (Code: given
Matrix: (-0.990974, -0.134053, -0.000499), (-0.133894, 0.989602, 0.052547), (-0.00655, 0.05214, -0.998618)
Vector: 0.27854, -0.84641, 32.3048)

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Components

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


Mass: 27291.855 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 206 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 206 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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 170MM (NH4)2SO4, 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2008 / Details: MIRROR
RadiationMonochromator: SILICON 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.85→49 Å / Num. obs: 44404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.88 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 5.93 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.26 / % possible all: 99.7

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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: 1.85→39.687 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 2247 5.1 %
Rwork0.1567 --
obs0.1586 44385 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.26 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.083 Å20 Å21.8133 Å2
2--8.4281 Å2-0 Å2
3----5.3451 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 86 429 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163720
X-RAY DIFFRACTIONf_angle_d1.5745038
X-RAY DIFFRACTIONf_dihedral_angle_d17.7241340
X-RAY DIFFRACTIONf_chiral_restr0.119498
X-RAY DIFFRACTIONf_plane_restr0.008652
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A43X-RAY DIFFRACTIONPOSITIONAL
12B43X-RAY DIFFRACTIONPOSITIONAL0.062
21A796X-RAY DIFFRACTIONPOSITIONAL
22B796X-RAY DIFFRACTIONPOSITIONAL0.035
31A850X-RAY DIFFRACTIONPOSITIONAL
32B850X-RAY DIFFRACTIONPOSITIONAL0.197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8499-1.890100.19222720X-RAY DIFFRACTION99
1.8901-1.93410.1585140.18912750X-RAY DIFFRACTION100
1.9341-1.98240.24052690.16952501X-RAY DIFFRACTION100
1.9824-2.0360.23512520.17452490X-RAY DIFFRACTION100
2.036-2.09590.1717220.16492724X-RAY DIFFRACTION100
2.0959-2.16360.19682560.16452518X-RAY DIFFRACTION100
2.1636-2.240900.16112779X-RAY DIFFRACTION100
2.2409-2.33060.2132180.16762530X-RAY DIFFRACTION100
2.3306-2.43670.20122030.16252583X-RAY DIFFRACTION100
2.4367-2.56510.21061850.16752574X-RAY DIFFRACTION100
2.5651-2.72580.23571440.1652636X-RAY DIFFRACTION100
2.7258-2.93620.21211350.1622638X-RAY DIFFRACTION100
2.9362-3.23160.18731170.16322673X-RAY DIFFRACTION100
3.2316-3.69890.1988980.14462695X-RAY DIFFRACTION100
3.6989-4.65910.15362010.12572591X-RAY DIFFRACTION100
4.6591-39.69620.14531330.1382736X-RAY DIFFRACTION100

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