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- PDB-1lc3: Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex -

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Basic information

Entry
Database: PDB / ID: 1lc3
TitleCrystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex
ComponentsBiliverdin Reductase A
KeywordsOXIDOREDUCTASE / Biliverdin Reductase / Tetrapyrrole / Bile Pigment / Bilirubin / Heme / NADH
Function / homology
Function and homology information


biliverdin reductase / biliverdin reductase [NAD(P)+] activity / biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / Heme degradation / Cytoprotection by HMOX1 / heme catabolic process / nucleotide binding / zinc ion binding / cytosol
Similarity search - Function
Biliverdin reductase, catalytic / Biliverdin reductase A / Biliverdin reductase, catalytic / : / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Biliverdin reductase, catalytic / Biliverdin reductase A / Biliverdin reductase, catalytic / : / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Biliverdin reductase A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsWhitby, F.G. / Phillips, J.D. / Hill, C.P. / McCoubrey, W. / Maines, M.D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of a biliverdin IXalpha reductase enzyme-cofactor complex.
Authors: Whitby, F.G. / Phillips, J.D. / Hill, C.P. / McCoubrey, W. / Maines, M.D.
History
DepositionApr 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHOR STATES THE PROTEIN WAS EXPRESSED AS AN N-TERMINALLY MODIFIED PROTEIN AS AN AID IN EXPRESSION

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biliverdin Reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9976
Polymers33,3851
Non-polymers1,6125
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.780, 76.140, 75.010
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 A / Biliverdin-IX alpha-reductase


Mass: 33385.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P46844, biliverdin reductase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2.0 M Na+/K+ phosphate, 100 mM CAPS, 200 mM lithium sulfate (Emerald Screen Wizard-I condition 27), pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.5 mg/mlprotein1drop
22.0 Msodium potassium phosphate1reservoir
3100 mMCAPS1reservoirpH10.5
4200 mMlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 47157 / Num. obs: 47157 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Biso Wilson estimate: 16.1 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 131242 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.5→24.47 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1301781.36 / Data cutoff high rms absF: 1301781.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 933 2 %RANDOM
Rwork0.214 ---
all-46819 --
obs-46819 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2531 Å2 / ksol: 0.381656 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---1.94 Å20 Å2
3---1.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 103 262 2693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d3.86
LS refinement shellResolution: 1.5→1.51 Å / Rfactor Rfree error: 0.082 / Total num. of bins used: 36
RfactorNum. reflection% reflection
Rfree0.337 17 1.4 %
Rwork0.293 1170 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NADH_RELAXED.PARAMETERNADH.TOPOLOGY
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PO4.PARPO4.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection Rfree: 1549 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / Rfactor Rwork: 0.293

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