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- PDB-5ooh: Human biliverdin IX beta reductase: NADP/Erythrosin extra bluish ... -

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Basic information

Entry
Database: PDB / ID: 5ooh
TitleHuman biliverdin IX beta reductase: NADP/Erythrosin extra bluish ternary complex
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / Biliverdin reductase
Function / homology
Function and homology information


FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation ...FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / peptidyl-cysteine S-nitrosylase activity / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Erythrosin / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsManso, J.A. / Pereira, P.J.B.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: In silicoand crystallographic studies identify key structural features of biliverdin IX beta reductase inhibitors having nanomolar potency.
Authors: Nesbitt, N.M. / Zheng, X. / Li, Z. / Manso, J.A. / Yen, W.Y. / Malone, L.E. / Ripoll-Rozada, J. / Pereira, P.J.B. / Mantle, T.J. / Wang, J. / Bahou, W.F.
History
DepositionAug 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 21, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8204
Polymers22,1481
Non-polymers1,6713
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-5 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.263, 40.259, 107.231
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 Flavin reductase (NADPH) / FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / ...FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / GHBP / NADPH-dependent diaphorase / NADPH-flavin reductase / FLR


Mass: 22148.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-9ZZ / Erythrosin


Mass: 835.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H8I4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5. NADP ADDED TO A FINAL CONCENTRATION OF 2.5 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→40.3 Å / Num. obs: 65182 / % possible obs: 96.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 3.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Rrim(I) all: 0.111 / Net I/σ(I): 15.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3061 / CC1/2: 0.808 / Rpim(I) all: 0.308 / Rrim(I) all: 0.893 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDO

1hdo


Resolution: 1.2→32.194 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 12.45
RfactorNum. reflection% reflection
Rfree0.1474 6190 4.99 %
Rwork0.122 --
obs0.1232 124155 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→32.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 83 319 1937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111739
X-RAY DIFFRACTIONf_angle_d1.2972404
X-RAY DIFFRACTIONf_dihedral_angle_d22.351656
X-RAY DIFFRACTIONf_chiral_restr0.089276
X-RAY DIFFRACTIONf_plane_restr0.009343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21370.26912260.25663685X-RAY DIFFRACTION92
1.2137-1.22790.26041770.23073922X-RAY DIFFRACTION94
1.2279-1.24290.27571860.21213840X-RAY DIFFRACTION94
1.2429-1.25860.19651940.1933821X-RAY DIFFRACTION93
1.2586-1.27520.20541890.17623870X-RAY DIFFRACTION95
1.2752-1.29270.18592200.16623806X-RAY DIFFRACTION94
1.2927-1.31110.19722040.15783875X-RAY DIFFRACTION95
1.3111-1.33070.1671950.15423927X-RAY DIFFRACTION95
1.3307-1.35150.17971530.14583853X-RAY DIFFRACTION94
1.3515-1.37370.14552600.14413848X-RAY DIFFRACTION96
1.3737-1.39740.15792200.13543847X-RAY DIFFRACTION95
1.3974-1.42280.15032030.13513897X-RAY DIFFRACTION96
1.4228-1.45010.15681710.12243971X-RAY DIFFRACTION96
1.4501-1.47970.14531850.11483931X-RAY DIFFRACTION96
1.4797-1.51190.1311900.09763938X-RAY DIFFRACTION96
1.5119-1.54710.1091980.09123939X-RAY DIFFRACTION96
1.5471-1.58580.11012190.08763936X-RAY DIFFRACTION97
1.5858-1.62860.11672140.08763934X-RAY DIFFRACTION97
1.6286-1.67660.12872620.08823911X-RAY DIFFRACTION96
1.6766-1.73070.13121890.09093948X-RAY DIFFRACTION98
1.7307-1.79250.11751980.09164026X-RAY DIFFRACTION98
1.7925-1.86430.12122300.09343969X-RAY DIFFRACTION98
1.8643-1.94910.13372080.08793987X-RAY DIFFRACTION98
1.9491-2.05190.10442340.09134012X-RAY DIFFRACTION98
2.0519-2.18040.10132080.08743988X-RAY DIFFRACTION99
2.1804-2.34870.1182190.09244054X-RAY DIFFRACTION99
2.3487-2.5850.13172090.10554015X-RAY DIFFRACTION99
2.585-2.95880.15652070.12034071X-RAY DIFFRACTION99
2.9588-3.72690.14132020.12584092X-RAY DIFFRACTION100
3.7269-32.20530.18622200.15174052X-RAY DIFFRACTION100

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