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- PDB-2vck: Structure of Phycoerythrobilin Synthase PebS from the Cyanophage ... -

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Basic information

Entry
Database: PDB / ID: 2vck
TitleStructure of 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: 1.8 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
DepositionSep 25, 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 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)112,8158
Polymers110,4844
Non-polymers2,3314
Water10,359575
1
A: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers27,6211
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers27,6211
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers27,6211
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CYANOBACTERIAL PHYCOERYTHROBILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers27,6211
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.560, 67.570, 81.280
Angle α, β, γ (deg.)92.26, 109.07, 106.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRVALVAL4AA22 - 5222 - 52
21THRTHRVALVAL4BB22 - 5222 - 52
31THRTHRVALVAL4CC22 - 5222 - 52
41THRTHRVALVAL4DD22 - 5222 - 52
12GLYGLYASPASP4AA57 - 13757 - 137
22GLYGLYASPASP4BB57 - 13757 - 137
32GLYGLYASPASP4CC57 - 13757 - 137
42GLYGLYASPASP4DD57 - 13757 - 137
13GLYGLYTHRTHR4AA147 - 203147 - 203
23GLYGLYTHRTHR4BB147 - 203147 - 203
33GLYGLYTHRTHR4CC147 - 203147 - 203
43GLYGLYTHRTHR4DD147 - 203147 - 203
14VALVALLYSLYS4AA208 - 233208 - 233
24VALVALLYSLYS4BB208 - 233208 - 233
34VALVALLYSLYS4CC208 - 233208 - 233
44VALVALLYSLYS4DD208 - 233208 - 233
15LYSLYSLYSLYS5AA2121
25LYSLYSLYSLYS5BB2121
35LYSLYSLYSLYS5CC2121
45LYSLYSLYSLYS5DD2121

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: 27621.107 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.: 575 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 51 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP VAPOUR DIFFUSION PROTEIN:RESERVOIR 2:1, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97887
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 1.8→49 Å / Num. obs: 91993 / % possible obs: 97.1 % / Observed criterion σ(I): 5 / Redundancy: 8.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5 / % possible all: 95.9

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Processing

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

2vcl


Resolution: 1.8→49.21 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.473 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4819 5.2 %RANDOM
Rwork0.184 ---
obs0.187 87171 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: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20.17 Å2
2--0.57 Å20.45 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 172 575 7675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9749985
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.0210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34914.9221246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2581530
X-RAY DIFFRACTIONr_chiral_restr0.1070.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025786
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.23443
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24892
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2576
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0611.54296
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52226791
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23333564
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2484.53188
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1569medium positional0.360.5
2B1569medium positional0.30.5
3C1569medium positional0.330.5
4D1569medium positional0.370.5
1A5loose positional3.35
2B5loose positional4.055
3C5loose positional3.455
4D5loose positional3.845
1A1569medium thermal0.872
2B1569medium thermal1.132
3C1569medium thermal1.12
4D1569medium thermal0.892
1A5loose thermal1.710
2B5loose thermal1.6910
3C5loose thermal0.710
4D5loose thermal0.4510
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.219 6763 -
Rfree-0 -
obs--100 %

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