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- PDB-2vgr: Structure of the WT-Phycoerythrobilin Synthase PebS from the Cyan... -

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Basic information

Entry
Database: PDB / ID: 2vgr
TitleStructure of the WT-Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex with the bound Substrate Biliverdin IXa
ComponentsCYANOBACTERIAL PHYCOERYTHROBILIN
KeywordsOXIDOREDUCTASE / CYANOPHAGES / BILIVERDIN IXA / PHYCOBILIN REDUCTASE / PHYCOBILIN SYNTHESIS / PROCHLOROCOCCUS / PHYCOERYTHROBILIN / BILIVERDIN REDUCTASE / FERREDOXIN DEPENDENT
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: 2.1 Å
AuthorsDammeyer, T. / Hofmann, E. / Frankenberg-Dinkel, N.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Phycoerythrobilin Synthase (Pebs) of a Marine Virus: Crystal Structures of the Biliverdin Complex and the Substrate-Free Form.
Authors: Dammeyer, T. / Hofmann, E. / Frankenberg-Dinkel, N.
History
DepositionNov 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYANOBACTERIAL PHYCOERYTHROBILIN
B: CYANOBACTERIAL PHYCOERYTHROBILIN
C: CYANOBACTERIAL PHYCOERYTHROBILIN
D: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5028
Polymers109,1714
Non-polymers2,3314
Water6,107339
1
A: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8752
Polymers27,2931
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8752
Polymers27,2931
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8752
Polymers27,2931
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8752
Polymers27,2931
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.990, 70.040, 81.670
Angle α, β, γ (deg.)75.53, 70.74, 71.13
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22C
13B
23D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRASNASNAA22 - 5122 - 51
211THRTHRASNASNBB22 - 5122 - 51
311THRTHRASNASNCC22 - 5122 - 51
411THRTHRASNASNDD22 - 5122 - 51
121GLYGLYPROPROAA57 - 13557 - 135
221GLYGLYPROPROBB57 - 13557 - 135
321GLYGLYPROPROCC57 - 13557 - 135
421GLYGLYPROPRODD57 - 13557 - 135
131ASNASNTHRTHRAA148 - 203148 - 203
231ASNASNTHRTHRBB148 - 203148 - 203
331ASNASNTHRTHRCC148 - 203148 - 203
431ASNASNTHRTHRDD148 - 203148 - 203
141ASPASPLYSLYSAA227 - 233227 - 233
241ASPASPLYSLYSBB227 - 233227 - 233
341ASPASPLYSLYSCC227 - 233227 - 233
441ASPASPLYSLYSDD227 - 233227 - 233
112PHEPHEGLYGLYAA144 - 147144 - 147
212PHEPHEGLYGLYCC144 - 147144 - 147
122GLUGLUASNASNAA204 - 226204 - 226
222GLUGLUASNASNCC204 - 226204 - 226
113GLYGLYASNASNBB210 - 226210 - 226
213GLYGLYASNASNDD210 - 226210 - 226

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.991, -0.13379, -0.00458), (0.1277, -0.93448, -0.33232), (0.04018, -0.32992, 0.94315)-20.4309, 31.99888, 8.9747
2given(0.99979, -0.01746, -0.01064), (-0.01756, -0.9998, -0.0091), (-0.01048, 0.00928, -0.9999)2.28744, 35.183, -20.05858
3given(-0.99055, -0.13704, -0.00617), (-0.12997, 0.92317, 0.36174), (-0.04388, 0.35912, -0.93226)-22.73905, 3.98705, -28.78696

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Components

#1: Protein
CYANOBACTERIAL PHYCOERYTHROBILIN / PHYCOBILIN REDUCTASE / CYANOPHAGE PHYCOERYTHROBILIN SYNTHASE PEBS


Mass: 27292.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLOROCOCCUS PHAGE P-SSM2 (virus) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98011
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 60138 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.3 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VCK

2vck


Resolution: 2.1→47.62 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.641 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3185 5.3 %RANDOM
Rwork0.226 ---
obs0.23 56953 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.59 Å20.4 Å2
2--3.76 Å2-1.08 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 172 339 7521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227387
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9759992
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32414.9221245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1391528
X-RAY DIFFRACTIONr_chiral_restr0.1180.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.23597
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.24905
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2484
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8091.54328
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36926817
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.60733551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2884.53175
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1429medium positional0.360.5
12B1429medium positional0.310.5
13C1429medium positional0.340.5
14D1429medium positional0.390.5
21A217medium positional0.320.5
31B135medium positional0.340.5
11A1429medium thermal0.872
12B1429medium thermal0.852
13C1429medium thermal0.782
14D1429medium thermal0.962
21A217medium thermal0.62
31B135medium thermal0.422
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.261 4460
Rfree-0

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