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- PDB-1he4: Human biliverdin IX beta reductase: NADP/FMN ternary complex -

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Basic information

Entry
Database: PDB / ID: 1he4
TitleHuman biliverdin IX beta reductase: NADP/FMN ternary complex
ComponentsBILIVERDIN IX BETA REDUCTASE
KeywordsBILIVERDIN-IX BETA REDUCTASE / FOETAL METABOLISM / HAEM DEGRADATION / FLAVIN REDUCTASE / DIAPHORASE / GREEN HAEM BINDING PROTEIN / METHAEMOGLOBIN REDUCTASE / ALPHA/BETA DINUCLEOTIDE BINDING FOLD
Function / homology
Function and homology information


biliberdin reductase NAD+ activity / biliverdin reductase (NADPH) activity / biliverdin reductase / biliverdin reductase (NAD(P)H) activity / flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / terminal bouton / Cytoprotection by HMOX1 ...biliberdin reductase NAD+ activity / biliverdin reductase (NADPH) activity / biliverdin reductase / biliverdin reductase (NAD(P)H) activity / flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / terminal bouton / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / 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
FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPereira, P.J.B. / Macedo-Ribeiro, S. / Parraga, A. / Perez-Luque, R. / Cunningham, O. / Darcy, K. / Mantle, T.J. / Coll, M.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of Human Biliverdin Ix Beta Reductase, an Early Fetal Bilirubin Ix Producing Enzyme
Authors: Pereira, P.J.B. / Macedo-Ribeiro, S. / Parraga, A. / Perez-Luque, R. / Cunningham, O. / Darcy, K. / Mantle, T.J. / Coll, M.
History
DepositionNov 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 22, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Other / Refinement description
Category: atom_site / pdbx_database_proc ...atom_site / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.1Dec 13, 2023Group: 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

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Assembly

Deposited unit
A: BILIVERDIN IX BETA REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3483
Polymers22,1481
Non-polymers1,2002
Water5,549308
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.100, 49.300, 106.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein BILIVERDIN IX BETA REDUCTASE / FLAVIN REDUCTASE (EC 1.6.99.1) / NADPH-DEPENDENT DIAPHORASE / NADPH-FLAVIN REDUCTASE / BILIVERDIN ...FLAVIN REDUCTASE (EC 1.6.99.1) / NADPH-DEPENDENT DIAPHORASE / NADPH-FLAVIN REDUCTASE / BILIVERDIN REDUCTASE B / GREEN HEME BINDING PROTEIN


Mass: 22148.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30043, biliverdin reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PDB ENTRY CONTAINS AN EXTRA N-TERMINAL METHIONINE

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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: 40.4 %
Crystal growpH: 6.5
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
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.7 mg/mlprotein1drop
22.5 mMNADP1drop
35 %(w/v)PEG80001drop
40.03 Mammonium sulfate1drop
50.02 Msodium cacodylate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorDate: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→44.7 Å / Num. obs: 42072 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.7
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.182 / % possible all: 95
Reflection
*PLUS
Num. measured all: 255020

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDO

1hdo


Resolution: 1.4→20 Å / Num. parameters: 17736 / Num. restraintsaints: 21375 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2107 5 %RANDOM
all0.138 42068 --
obs0.134 -98.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1900.47
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 79 308 1928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0278
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.001
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.019
X-RAY DIFFRACTIONs_approx_iso_adps0.085
Software
*PLUS
Name: SHELXL-97/2 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.0278
X-RAY DIFFRACTIONs_chiral_restr0.059

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