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- PDB-8ell: Apo human biliverdin reductase beta (cryogenic) -

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Basic information

Entry
Database: PDB / ID: 8ell
TitleApo human biliverdin reductase beta (cryogenic)
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / Apo / cryogenic
Function / homology
Function and homology information


biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process ...biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / 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 domain superfamily
Similarity search - Domain/homology
Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsMcLeod, M.J. / Eisenmesser, E.Z. / Lee, E. / Thorne, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139892 United States
CitationJournal: Front Mol Biosci / Year: 2023
Title: Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle.
Authors: Lee, E. / McLeod, M.J. / Redzic, J.S. / Marcolin, B. / Thorne, R.E. / Agarwal, P. / Eisenmesser, E.Z.
History
DepositionSep 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)22,1943
Polymers22,1481
Non-polymers462
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.187, 45.668, 104.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 1-4% PEG 20000. Equilibrated over 0.25-0.5 M NaCl. BLVRB 18 mg/mL.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1.1271 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.52→52.1 Å / Num. obs: 31069 / % possible obs: 97.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 14.34 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Rrim(I) all: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2891 / CC1/2: 0.743 / CC star: 0.923 / Rpim(I) all: 0.338 / Rrim(I) all: 1.085 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OPL

6opl


Resolution: 1.52→52.1 Å / SU ML: 0.175 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1875 1561 5.02 %
Rwork0.1595 29507 -
obs0.1609 31068 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 1.52→52.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 2 325 1871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771735
X-RAY DIFFRACTIONf_angle_d0.97462385
X-RAY DIFFRACTIONf_chiral_restr0.0657278
X-RAY DIFFRACTIONf_plane_restr0.0096316
X-RAY DIFFRACTIONf_dihedral_angle_d12.2595652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.570.25511260.22622451X-RAY DIFFRACTION91.03
1.57-1.620.24191470.1922601X-RAY DIFFRACTION96.05
1.62-1.690.20731240.17922646X-RAY DIFFRACTION97.33
1.69-1.770.23081280.16992651X-RAY DIFFRACTION97.65
1.77-1.860.20181320.1692660X-RAY DIFFRACTION98.31
1.86-1.980.2151560.17622681X-RAY DIFFRACTION98.51
1.98-2.130.17371250.15632698X-RAY DIFFRACTION98.02
2.13-2.340.19041200.15252739X-RAY DIFFRACTION98.96
2.34-2.680.20171750.16642709X-RAY DIFFRACTION99.24
2.68-3.380.18561440.15272770X-RAY DIFFRACTION99.52
3.38-52.10.15261840.14142901X-RAY DIFFRACTION99.55
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.52753771372-0.1817836774210.5080237377451.80347741388-0.07607216232962.359578987350.04850334718150.0525490803314-0.0749721754312-0.172381131737-0.004895967100120.02001513456380.1919882835640.0573782356658-0.02636560162650.1080120979840.0158833139957-0.0007527353403820.07280629599970.0002552667109190.073814773173416.5344609231-8.7515844851215.4584009736
24.03190452076-0.9548082896890.4039547776370.794177149161-0.205288776960.678485606118-0.02788906140370.007201102317620.08268348329290.03256437162170.003125687114170.0157383909332-0.0233848758861-0.0452728284710.02486108873960.106202666646-0.008831756300510.001365006590870.0790149843086-0.001767112951410.086014258675110.62261660845.6422492849418.5428214991
33.50172827910.572901941582-2.939950942150.312404741822-0.5666137684612.409159747820.0381312162751-0.1942799147770.1664963978830.0336146330498-0.002426527918560.00922088695981-0.0579550784980.090806699354-0.06944333837060.09888604381770.00831603052634-0.009042631077660.0977795879131-0.008292675615140.0970586384795.2715115564311.157884800620.2435188149
42.368413250080.7752664980431.216911252592.720012420320.1179235367351.603691663740.2123226937320.2000516667-0.00254271293375-0.137947379357-0.04020099607390.2133701390140.234867705571-0.0125387115689-0.0884184061280.1371028123530.0131913744901-0.01161314092450.1101634434680.006352657728280.07363840752833.826498809215.228341012264.8959253659
52.230661444791.979199136791.05393438822.257746538550.2873560945661.344068563720.08275659848230.132564776611-0.178812153759-0.332561033293-0.05453942934030.0319726323090.2126430450790.0655959588353-0.06673726341760.1849531502490.0254373128281-0.03941060554440.1041055293040.001672072434850.0975968933117.78145203385-1.242467289514.36553880633
62.13896009423-0.598448955325-0.5655286091462.519774340370.4050910698853.159337332410.197080690870.0713073409267-0.0657159745111-0.299726701228-0.142980028150.1299222192550.148997913751-0.0542100756317-0.03622960047920.1875052522850.0135822162004-0.03224938980580.09140353035050.03792509926230.08241955707586.878531715796.014371264892.0236301005
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 57 )2 - 571 - 56
22chain 'A' and (resid 58 through 122 )58 - 12257 - 121
33chain 'A' and (resid 123 through 142 )123 - 142122 - 141
44chain 'A' and (resid 143 through 174 )143 - 174142 - 173
55chain 'A' and (resid 175 through 189 )175 - 189174 - 188
66chain 'A' and (resid 190 through 206 )190 - 206189 - 205

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