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- PDB-5b3v: Crystal structure of biliverdin reductase in complex with biliver... -

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Basic information

Entry
Database: PDB / ID: 5b3v
TitleCrystal structure of biliverdin reductase in complex with biliverdin and NADP+ from Synechocystis sp. PCC 6803
ComponentsBiliverdin reductase
KeywordsTRANSFERASE / biliverdin reductase / heme degrading pathway / NAD(P)H-dependent enzyme / tetrapyrrole / Rossmann fold
Function / homology
Function and homology information


: / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Biliverdin reductase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsTakao, H. / Wada, K.
Citation
Journal: Nat Commun / Year: 2017
Title: A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity
Authors: Takao, H. / Hirabayashi, K. / Nishigaya, Y. / Kouriki, H. / Nakaniwa, T. / Hagiwara, Y. / Harada, J. / Sato, H. / Yamazaki, T. / Sakakibara, Y. / Suiko, M. / Asada, Y. / Takahashi, Y. / ...Authors: Takao, H. / Hirabayashi, K. / Nishigaya, Y. / Kouriki, H. / Nakaniwa, T. / Hagiwara, Y. / Harada, J. / Sato, H. / Yamazaki, T. / Sakakibara, Y. / Suiko, M. / Asada, Y. / Takahashi, Y. / Yamamoto, K. / Fukuyama, K. / Sugishima, M. / Wada, K.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Expression, purification and preliminary X-ray crystallographic analysis of cyanobacterial biliverdin reductase.
Authors: Watanabe, A. / Hirata, K. / Hagiwara, Y. / Yutani, Y. / Sugishima, M. / Yamamoto, M. / Fukuyama, K. / Wada, K.
History
DepositionMar 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 11, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Biliverdin reductase
A: Biliverdin reductase
C: Biliverdin reductase
D: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,49016
Polymers147,8554
Non-polymers7,63512
Water4,089227
1
B: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.500, 100.413, 138.028
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Biliverdin reductase


Mass: 36963.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: bvdR / Production host: Escherichia coli (E. coli) / References: UniProt: P72782
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG4000, Trizma (pH8.2), magnesium chloride, barium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.594→50 Å / Num. obs: 46736 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 19.83 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3T

5b3t


Resolution: 2.594→49.624 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 2216 4.77 %
Rwork0.208 --
obs0.2103 46428 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.594→49.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9993 0 536 227 10756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510789
X-RAY DIFFRACTIONf_angle_d1.76114703
X-RAY DIFFRACTIONf_dihedral_angle_d15.2946191
X-RAY DIFFRACTIONf_chiral_restr0.0731557
X-RAY DIFFRACTIONf_plane_restr0.0041877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.594-2.65040.36341270.26952506X-RAY DIFFRACTION89
2.6504-2.7120.29471440.26162697X-RAY DIFFRACTION98
2.712-2.77980.30341400.2612783X-RAY DIFFRACTION99
2.7798-2.8550.32581590.2562716X-RAY DIFFRACTION100
2.855-2.9390.26811400.25412824X-RAY DIFFRACTION100
2.939-3.03380.29191470.24352711X-RAY DIFFRACTION100
3.0338-3.14230.34031330.24462781X-RAY DIFFRACTION100
3.1423-3.2680.31661290.23812815X-RAY DIFFRACTION100
3.268-3.41670.28491200.23112787X-RAY DIFFRACTION100
3.4167-3.59680.26571130.2112803X-RAY DIFFRACTION100
3.5968-3.82210.23361300.18932783X-RAY DIFFRACTION100
3.8221-4.11710.21751370.18562770X-RAY DIFFRACTION100
4.1171-4.53120.21891460.16382797X-RAY DIFFRACTION100
4.5312-5.18620.23281390.16512808X-RAY DIFFRACTION100
5.1862-6.53170.23781380.19082818X-RAY DIFFRACTION100
6.5317-49.63260.1911740.1672813X-RAY DIFFRACTION99

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