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- PDB-6opl: Human biliverdin IX beta reductase Q14R mutant: NADP complex -

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Basic information

Entry
Database: PDB / ID: 6opl
TitleHuman biliverdin IX beta reductase Q14R mutant: NADP complex
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / Human biliverdin IX beta reductase / short-chain dehydrogenase/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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPaukovich, N.A. / Eisenmesser, E.Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Controlling biliverdin reductase B coenzyme binding through evolution
Authors: Paukovich, N.A. / Eisenmesser, E.Z.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7932
Polymers22,0491
Non-polymers7431
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-2 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.163, 98.145, 125.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

21A-830-

HOH

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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: 22049.283 Da / Num. of mol.: 1 / Mutation: Q14R
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: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: mother liquor: 0.1 M MES monohydrate, 12% w/v PEG20000, 1 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→39.98 Å / Num. obs: 55280 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Χ2: 0.97 / Net I/σ(I): 15.6
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 4 % / Rmerge(I) obs: 2.133 / Num. unique obs: 2685 / CC1/2: 0.317 / Χ2: 0.73 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HDO

1hdo


Resolution: 1.37→38.697 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.33
RfactorNum. reflection% reflection
Rfree0.2617 2967 2.69 %
Rwork0.2323 --
obs0.233 50913 88.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.37→38.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 48 247 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111632
X-RAY DIFFRACTIONf_angle_d1.5252234
X-RAY DIFFRACTIONf_dihedral_angle_d18.574599
X-RAY DIFFRACTIONf_chiral_restr0.095266
X-RAY DIFFRACTIONf_plane_restr0.008280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.32140.6483180.6781358X-RAY DIFFRACTION6
1.3214-1.34420.5694510.5111781X-RAY DIFFRACTION31
1.3442-1.36860.5275980.48693207X-RAY DIFFRACTION56
1.3686-1.39490.47591280.42764489X-RAY DIFFRACTION78
1.3949-1.42340.41481480.39685481X-RAY DIFFRACTION95
1.4234-1.45430.4031560.35575690X-RAY DIFFRACTION99
1.4543-1.48820.28841550.32635685X-RAY DIFFRACTION100
1.4882-1.52540.3251580.30545764X-RAY DIFFRACTION100
1.5254-1.56660.25951610.2885745X-RAY DIFFRACTION100
1.5666-1.61270.3291550.27725759X-RAY DIFFRACTION100
1.6127-1.66480.27591600.26085697X-RAY DIFFRACTION100
1.6648-1.72430.26211590.24645774X-RAY DIFFRACTION100
1.7243-1.79330.27711590.23345751X-RAY DIFFRACTION100
1.7933-1.8750.22821550.22395721X-RAY DIFFRACTION100
1.875-1.97380.25691590.21835740X-RAY DIFFRACTION100
1.9738-2.09750.23971560.20415779X-RAY DIFFRACTION100
2.0975-2.25940.22731560.20265697X-RAY DIFFRACTION100
2.2594-2.48670.25671600.25798X-RAY DIFFRACTION100
2.4867-2.84650.24041570.21335740X-RAY DIFFRACTION100
2.8465-3.58580.22561610.20865757X-RAY DIFFRACTION100
3.5858-38.71390.25021570.21285723X-RAY DIFFRACTION100

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