[English] 日本語
Yorodumi
- PDB-4h2d: Crystal structure of NDOR1 -

+
Open data


ID or keywords:

Loading...

-
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 / cellular response to menadione / cell death / Cytosolic iron-sulfur cluster assembly / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / NADPH-hemoprotein reductase activity / intermediate filament cytoskeleton / iron-sulfur cluster assembly / FMN binding ...Oxidoreductases; Acting on iron-sulfur proteins as donors; With NAD+ or NADP+ as acceptor / cellular response to menadione / cell death / Cytosolic iron-sulfur cluster assembly / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / NADPH-hemoprotein reductase activity / intermediate filament cytoskeleton / iron-sulfur cluster assembly / FMN binding / NADP binding / flavin adenine dinucleotide binding / oxidoreductase 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more