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- PDB-8elm: Apo human biliverdin reductase beta (293K) -

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Basic information

Entry
Database: PDB / ID: 8elm
TitleApo human biliverdin reductase beta (293K)
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / Apo / Room-temperature
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: 2.19 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)22,1712
Polymers22,1481
Non-polymers231
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area9780 Å2
Unit cell
Length a, b, c (Å)42.591, 47.309, 101.075
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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.3 Å3/Da / Density % sol: 46.49 % / Description: Thin needles.
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.19→50.5 Å / Num. obs: 10970 / % possible obs: 99.3 % / Redundancy: 12.4 % / Biso Wilson estimate: 33.57 Å2 / CC1/2: 0.969 / CC star: 0.992 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.086 / Rrim(I) all: 0.301 / Net I/σ(I): 8.24
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1065 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.379 / Rrim(I) all: 1.352 / % possible all: 97.4

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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: 2.19→50.5 Å / SU ML: 0.2143 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 545 4.97 %
Rwork0.1752 10425 -
obs0.1775 10970 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.67 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 1 49 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171626
X-RAY DIFFRACTIONf_angle_d0.42272223
X-RAY DIFFRACTIONf_chiral_restr0.0425262
X-RAY DIFFRACTIONf_plane_restr0.0032290
X-RAY DIFFRACTIONf_dihedral_angle_d9.7569596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.410.23941350.18792491X-RAY DIFFRACTION97.58
2.41-2.760.22391430.18822568X-RAY DIFFRACTION99.41
2.76-3.470.2391370.18692615X-RAY DIFFRACTION99.64
3.47-50.50.21641300.16312751X-RAY DIFFRACTION99.59
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)
13.65999270753-0.7209391794330.986026884794.17704593520.7260024544264.597511012440.0968841729292-0.10352918063-0.3524339124760.2219765694820.01522579968750.1100631603180.379708450254-0.0765183061026-0.09956570356660.220666318202-0.0285170088175-0.02412919946610.1701023638090.002796563755030.244735212549-17.9025871516-7.6606848788-15.077383695
22.54694850370.805091290326-0.2714941182280.3974246479150.3728010494911.52328539612-0.02766509608080.4521229935620.244061935543-0.067610737010.0911488434206-0.11287158558-0.01089141533910.138790761534-0.003085809788420.2551848053990.00911553957589-0.009426012229550.2883251197210.02822844802050.320318874041-7.112792605667.49304171732-19.5120448301
34.55076196421-0.4343486548150.8973802957044.83105744974-0.3913118715444.66603199325-0.032187156828-0.383156564147-0.03629788379470.1950429279880.102327741204-0.3725848999090.3136476450550.282814291913-0.05418453226040.265909192218-0.00592837980512-0.02996699395610.268093139073-0.03620759494730.241476526721-5.527964112883.70311240674-3.5174795772
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 73 )2 - 731 - 72
22chain 'A' and (resid 74 through 142 )74 - 14273 - 141
33chain 'A' and (resid 143 through 206 )143 - 206142 - 205

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