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- PDB-4h2d: Crystal structure of NDOR1 -

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Basic information

Entry
Database: PDB / ID: 4h2d
TitleCrystal structure of NDOR1
ComponentsNADPH-dependent diflavin oxidoreductase 1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on iron-sulfur proteins as donors; With NAD+ or NADP+ as acceptor / NADPH-iron-sulfur [2Fe-2S] protein oxidoreductase activity / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / Cytosolic iron-sulfur cluster assembly / NADPH-hemoprotein reductase activity / intermediate filament cytoskeleton / iron-sulfur cluster assembly / NADPH binding / FAD binding / electron transport chain ...Oxidoreductases; Acting on iron-sulfur proteins as donors; With NAD+ or NADP+ as acceptor / NADPH-iron-sulfur [2Fe-2S] protein oxidoreductase activity / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / Cytosolic iron-sulfur cluster assembly / NADPH-hemoprotein reductase activity / intermediate filament cytoskeleton / iron-sulfur cluster assembly / NADPH binding / FAD binding / electron transport chain / FMN binding / NADP binding / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer activity / perinuclear region of cytoplasm / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
NADPH-dependent diflavin oxidoreductase 1 / Flavodoxin domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase ...NADPH-dependent diflavin oxidoreductase 1 / Flavodoxin domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / 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 / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADPH-dependent diflavin oxidoreductase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBanci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mikolajczyk, M. / Jaiswal, D. / Winkelmann, J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Giachetti, A. / Jaiswal, D. / Mikolajczyk, M. / Piccioli, M. / Winkelmann, J.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: NADPH-cytochrome P450 oxidoreductase. Structural basis for hydride and electron transfer.
Authors: Hubbard, P.A. / Shen, A.L. / Paschke, R. / Kasper, C.B. / Kim, J.J.
#2: Journal: Biochemistry / Year: 2005
Title: Solution structure of the sulfite reductase flavodoxin-like domain from Escherichia coli.
Authors: Sibille, N. / Blackledge, M. / Brutscher, B. / Coves, J. / Bersch, B.
#3: Journal: J.Biol.Chem. / Year: 2009
Title: Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450.
Authors: Hamdane, D. / Xia, C. / Im, S.C. / Zhang, H. / Kim, J.J. / Waskell, L.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent diflavin oxidoreductase 1
B: NADPH-dependent diflavin oxidoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6034
Polymers36,6902
Non-polymers9132
Water2,684149
1
A: NADPH-dependent diflavin oxidoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8012
Polymers18,3451
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-dependent diflavin oxidoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8012
Polymers18,3451
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.450, 80.450, 101.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NADPH-dependent diflavin oxidoreductase 1 / NDOR1 / NADPH-dependent FMN and FAD-containing oxidoreductase / Novel reductase 1


Mass: 18345.115 Da / Num. of mol.: 2 / Fragment: FMN-binding domain (UNP residues 1-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDOR1, NR1 / Plasmid: Gateway pEntr-TEV-d-Topo pTH-34 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: Q9UHB4, Oxidoreductases; Acting on NADH or NADPH
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, 30% PEG5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2012 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.8→20.1 Å / Num. all: 31433 / Num. obs: 31433 / % possible obs: 99.7 % / Redundancy: 10.65 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 16.61
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4943 / Rsym value: 0.52 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JA1

1ja1


Resolution: 1.8→12.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.176 / SU ML: 0.087 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23387 1566 5 %RANDOM
Rwork0.21169 ---
all0.21278 29758 --
obs0.21278 29758 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→12.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 62 149 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2852.0043484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.96422.906117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45815409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1371526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211960
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 93 -
Rwork0.249 1896 -
obs--96.88 %
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)
10.05990.0837-0.02010.50760.16730.6656-0.02510.0222-0.0187-0.01340.03870.0328-0.03380.0327-0.01360.0320.0073-0.00050.0457-0.01530.075524.2304-2.2956-15.7737
20.39730.2228-0.04320.840.00810.99090.0568-0.00570.00880.1599-0.02680.0803-0.0056-0.0015-0.030.0975-0.00650.03150.0018-0.00930.056215.0499-14.28286.2452
30.11750.2135-0.11080.6029-0.00670.28170.0106-0.0080.01510.01780.01140.021-0.00760.0369-0.02190.0470.0067-0.01030.047-0.00950.058524.7341-5.7595-10.5873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 161
2X-RAY DIFFRACTION1A200
3X-RAY DIFFRACTION2B4 - 156
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3A301 - 408
6X-RAY DIFFRACTION3B301 - 341

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