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- PDB-1gcu: CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A -

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Basic information

Entry
Database: PDB / ID: 1gcu
TitleCRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A
ComponentsBILIVERDIN REDUCTASE A
KeywordsOXIDOREDUCTASE / biliverdin / Rossmann fold
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
Biliverdin reductase A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsKikuchi, A. / Park, S.Y. / Shiro, Y.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of rat biliverdin reductase.
Authors: Kikuchi, A. / Park, S.Y. / Miyatake, H. / Sun, D. / Sato, M. / Yoshida, T. / Shiro, Y.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BILIVERDIN REDUCTASE A


Theoretical massNumber of molelcules
Total (without water)33,6121
Polymers33,6121
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.682, 70.487, 87.866
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


Mass: 33611.535 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4, Na citrate, Na/K tartrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
20.2 Mpotassium sodium tartrate1reservoir
32.0 Mammonium sulfate1reservoir
44.3 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.4→32.71 Å / Num. all: 379020 / Num. obs: 379020 / Observed criterion σ(F): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.324 / Num. unique all: 9812 / % possible all: 94.3
Reflection
*PLUS
Num. obs: 71182 / Num. measured all: 379020

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.4→32.7 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3606 -RANDOM
Rwork0.219 ---
obs0.219 71120 98.2 %-
all-71120 --
Refinement stepCycle: LAST / Resolution: 1.4→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 294 2629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.6
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 32.7 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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