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- PDB-1qx4: Structrue of S127P mutant of cytochrome b5 reductase -

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Basic information

Entry
Database: PDB / ID: 1qx4
TitleStructrue of S127P mutant of cytochrome b5 reductase
ComponentsNADH-cytochrome b5 reductase
KeywordsOXIDOREDUCTASE / methemoglobinemia / flavin flexibility
Function / homology
Function and homology information


Phase I - Functionalization of compounds / nitric-oxide synthase complex / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / nitrite reductase (NO-forming) activity / Neutrophil degranulation / AMP binding / cholesterol biosynthetic process / nitric oxide biosynthetic process ...Phase I - Functionalization of compounds / nitric-oxide synthase complex / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / nitrite reductase (NO-forming) activity / Neutrophil degranulation / AMP binding / cholesterol biosynthetic process / nitric oxide biosynthetic process / FAD binding / lipid droplet / mitochondrial membrane / ADP binding / NAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type ...NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBewley, M.C. / Davis, C.A. / Marohnic, C.C. / Taormina, D. / Barber, M.J.
CitationJournal: Biochemistry / Year: 2003
Title: The structure of the S127P mutant of cytochrome b5 reductase that causes methemoglobinemia shows the AMP moiety of the flavin occupying the substrate binding site
Authors: Bewley, M.C. / Davis, C.A. / Marohnic, C.C. / Taormina, D. / Barber, M.J.
History
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-cytochrome b5 reductase
B: NADH-cytochrome b5 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2224
Polymers62,6502
Non-polymers1,5712
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.236, 48.004, 77.247
Angle α, β, γ (deg.)90.00, 107.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NADH-cytochrome b5 reductase


Mass: 31325.217 Da / Num. of mol.: 2 / Mutation: S127P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: DIA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon-Plus (DE3)RIL / References: UniProt: P20070, cytochrome-b5 reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: glycerol, ammonium sulfate, tris buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 48325 / Num. obs: 48325 / % possible obs: 96 % / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IB0 without FAD molecule

1ib0


Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 1014 random
Rwork0.207 --
all0.207 48320 -
obs0.207 48320 -
Solvent computationBsol: 24.0223 Å2 / ksol: 0.438183 e/Å3
Displacement parameters
Baniso -1Baniso -3Baniso -2
1--0.998 Å2-1.806 Å2-
2---1.299 Å2
3---0.301 Å2-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 106 256 4588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.2941.5
X-RAY DIFFRACTIONc_mcangle_it1.8472
X-RAY DIFFRACTIONc_scbond_it2.1682
X-RAY DIFFRACTIONc_scangle_it3.0342.5

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