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- PDB-5b3t: Crystal structure of apo-form biliverdin reductase from Synechocy... -

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Basic information

Entry
Database: PDB / ID: 5b3t
TitleCrystal structure of apo-form biliverdin reductase from Synechocystis sp. PCC 6803
ComponentsBiliverdin reductase
KeywordsTRANSFERASE / biliverdin reductase / heme degrading pathway / NAD(P)H-dependent enzyme / tetrapyrrole / Rossmann fold
Function / homology: / 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 / nucleotide binding / PHOSPHATE ION / Biliverdin reductase
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.099 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 12, 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: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / diffrn_radiation_wavelength
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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,3076
Polymers73,9282
Non-polymers3804
Water5,044280
1
A: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2494
Polymers36,9641
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0592
Polymers36,9641
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.248, 88.497, 133.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Biliverdin reductase


Mass: 36963.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: bvdR / Production host: Escherichia coli (E. coli) / References: UniProt: P72782
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG4000, Tris-HCl (pH7.25), Sodium acetate, Cymal-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→43.899 Å / Num. obs: 40823 / % possible obs: 99 % / Redundancy: 6.93 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 18.2
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.02 / % possible all: 95.1

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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: SIRAS / Resolution: 2.099→43.899 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 2000 4.91 %Random selection
Rwork0.1996 ---
obs0.2015 40758 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→43.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 20 280 5320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025145
X-RAY DIFFRACTIONf_angle_d0.6416976
X-RAY DIFFRACTIONf_dihedral_angle_d13.0513008
X-RAY DIFFRACTIONf_chiral_restr0.043761
X-RAY DIFFRACTIONf_plane_restr0.003911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0989-2.15140.29241290.24342501X-RAY DIFFRACTION91
2.1514-2.20960.27361400.24082713X-RAY DIFFRACTION98
2.2096-2.27460.26741420.22642748X-RAY DIFFRACTION100
2.2746-2.3480.26941420.2262746X-RAY DIFFRACTION100
2.348-2.43190.23351430.21952776X-RAY DIFFRACTION100
2.4319-2.52930.29211430.22272768X-RAY DIFFRACTION100
2.5293-2.64440.22511420.22052767X-RAY DIFFRACTION100
2.6444-2.78380.28831430.23012772X-RAY DIFFRACTION100
2.7838-2.95820.26821450.22412787X-RAY DIFFRACTION100
2.9582-3.18650.2571430.22282781X-RAY DIFFRACTION100
3.1865-3.50710.24981440.20432795X-RAY DIFFRACTION100
3.5071-4.01420.23981460.17942837X-RAY DIFFRACTION100
4.0142-5.05630.15741480.14962848X-RAY DIFFRACTION100
5.0563-43.90880.21891500.16442919X-RAY DIFFRACTION97

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