[English] 日本語
Yorodumi
- PDB-7jvl: Structure of the M101A variant of the SidA ornithine hydroxylase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jvl
TitleStructure of the M101A variant of the SidA ornithine hydroxylase complexed with NADP and the FAD in the "out" conformation
ComponentsL-ornithine N(5)-monooxygenase
KeywordsOXIDOREDUCTASE / FLAVIN-CONTAINING MONOOXYGENASE / FLAVOPROTEIN
Function / homology
Function and homology information


L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / NADP+ binding / secondary metabolite biosynthetic process ...L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / NADP+ binding / secondary metabolite biosynthetic process / monooxygenase activity / intracellular iron ion homeostasis / iron ion binding
Similarity search - Function
L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsTanner, J.J. / Campbell, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2003658 United States
National Science Foundation (NSF, United States)CHE-2003986 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Determinants of Flavin Dynamics in a Class B Monooxygenase.
Authors: Campbell, A.C. / Robinson, R. / Mena-Aguilar, D. / Sobrado, P. / Tanner, J.J.
History
DepositionAug 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-ornithine N(5)-monooxygenase
B: L-ornithine N(5)-monooxygenase
C: L-ornithine N(5)-monooxygenase
D: L-ornithine N(5)-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,26722
Polymers227,5984
Non-polymers6,66818
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26480 Å2
ΔGint-152 kcal/mol
Surface area66800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.229, 153.811, 89.870
Angle α, β, γ (deg.)90.000, 109.280, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 31 or (resid 32 through 33...
21(chain B and (resid 31 through 32 or (resid 33...
31(chain C and (resid 31 through 37 or (resid 38...
41(chain D and (resid 31 or (resid 32 through 33...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and (resid 31 or (resid 32 through 33...AA3131
12ARGARGSERSER(chain A and (resid 31 or (resid 32 through 33...AA32 - 3332 - 33
13ARGARGARGARG(chain A and (resid 31 or (resid 32 through 33...AA30 - 48930 - 489
14ARGARGARGARG(chain A and (resid 31 or (resid 32 through 33...AA30 - 48930 - 489
15ARGARGARGARG(chain A and (resid 31 or (resid 32 through 33...AA30 - 48930 - 489
16ARGARGARGARG(chain A and (resid 31 or (resid 32 through 33...AA30 - 48930 - 489
21LEULEUARGARG(chain B and (resid 31 through 32 or (resid 33...BB31 - 3231 - 32
22SERSERSERSER(chain B and (resid 31 through 32 or (resid 33...BB3333
23ARGARGGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB30 - 48830 - 488
24ARGARGGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB30 - 48830 - 488
25ARGARGGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB30 - 48830 - 488
26ARGARGGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB30 - 48830 - 488
31LEULEUASPASP(chain C and (resid 31 through 37 or (resid 38...CC31 - 3731 - 37
32GLUGLUGLUGLU(chain C and (resid 31 through 37 or (resid 38...CC3838
33LEULEUGLUGLU(chain C and (resid 31 through 37 or (resid 38...CC31 - 48831 - 488
34LEULEUGLUGLU(chain C and (resid 31 through 37 or (resid 38...CC31 - 48831 - 488
35LEULEUGLUGLU(chain C and (resid 31 through 37 or (resid 38...CC31 - 48831 - 488
36LEULEUGLUGLU(chain C and (resid 31 through 37 or (resid 38...CC31 - 48831 - 488
41LEULEULEULEU(chain D and (resid 31 or (resid 32 through 33...DD3131
42ARGARGSERSER(chain D and (resid 31 or (resid 32 through 33...DD32 - 3332 - 33
43ARGARGACTACT(chain D and (resid 31 or (resid 32 through 33...DD - T30 - 60330
44ARGARGACTACT(chain D and (resid 31 or (resid 32 through 33...DD - T30 - 60330
45ARGARGACTACT(chain D and (resid 31 or (resid 32 through 33...DD - T30 - 60330
46ARGARGACTACT(chain D and (resid 31 or (resid 32 through 33...DD - T30 - 60330

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
L-ornithine N(5)-monooxygenase / OMO / L-ornithine N(5)-oxygenase / Siderophore biosynthesis protein A


Mass: 56899.562 Da / Num. of mol.: 4 / Mutation: M101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: sidA, Afu2g07680 / Production host: Escherichia coli (E. coli)
References: UniProt: E9QYP0, L-ornithine N5-monooxygenase [NAD(P)H]

-
Non-polymers , 5 types, 589 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Enzyme stock solution: 8-10 mg/ml SidA (M101A) with 1 mM NADP+ in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium ...Details: Enzyme stock solution: 8-10 mg/ml SidA (M101A) with 1 mM NADP+ in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate. Cryo-buffer: 15 % PEG-200, 20 % PEG 3350, 0.1 M HEPES, (pH 7.5), 0.1 M calcium acetate. Drop ratio: 2 enzyme to 1 reservoir

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→62.89 Å / Num. obs: 115533 / % possible obs: 96.6 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 9.4 / Num. measured all: 401873 / Scaling rejects: 518
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.142.90.4451638056920.740.310.5461.795.9
11.5-62.893.60.02126847400.9990.0130.02530.298.4

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6X0I

6x0i


Resolution: 2.1→62.89 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 2208 1.96 %
Rwork0.2042 110712 -
obs0.2049 112920 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.78 Å2 / Biso mean: 28.5864 Å2 / Biso min: 13.03 Å2
Refinement stepCycle: final / Resolution: 2.1→62.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13765 0 438 571 14774
Biso mean--24.54 26.11 -
Num. residues----1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814534
X-RAY DIFFRACTIONf_angle_d0.98619771
X-RAY DIFFRACTIONf_dihedral_angle_d19.9255457
X-RAY DIFFRACTIONf_chiral_restr0.0562193
X-RAY DIFFRACTIONf_plane_restr0.0062522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6140X-RAY DIFFRACTION8.851TORSIONAL
12B6140X-RAY DIFFRACTION8.851TORSIONAL
13C6140X-RAY DIFFRACTION8.851TORSIONAL
14D6140X-RAY DIFFRACTION8.851TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.25491320.20477057718996
2.15-2.20.28791370.22587306744399
2.2-2.250.3837910.38164564465563
2.25-2.310.3631250.28896590671590
2.31-2.380.27931420.215172657407100
2.38-2.460.27991440.211772717415100
2.46-2.540.25081480.212873557503100
2.54-2.650.2861430.23987224736799
2.65-2.770.27741210.25276728684992
2.77-2.910.24271350.209773467481100
2.91-3.090.24891690.212473137482100
3.09-3.330.2321630.205572907453100
3.33-3.670.26391350.22896116625184
3.67-4.20.21031340.1826534666889
4.2-5.290.14041360.135973647500100
5.29-62.890.21191530.16537389754299
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)
10.72620.13220.00680.758-0.11910.49960.0544-0.1434-0.00650.0906-0.0232-0.095-0.01410.1109-0.02610.1606-0.0026-0.03150.2016-0.03890.1423117.1340.642851.5885
20.71370.2853-0.3090.6478-0.26270.5952-0.04050.0891-0.081-0.04180.05320.04020.056-0.0692-0.01890.13130.0037-0.0180.121-0.02230.16779.5462-21.039832.1655
30.621-0.1326-0.08960.9397-0.4630.94940.05240.11890.10110.07320.05350.177-0.2303-0.2378-0.07450.19490.06860.02220.19740.0280.21581.079623.725824.0531
40.65450.1297-0.24690.5249-0.26720.8508-0.02170.1585-0.0295-0.1036-0.0342-0.12810.10050.08690.05630.17050.03810.00950.2354-0.02920.1579118.34130.26826.2236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA30 - 489
2X-RAY DIFFRACTION2chain BB30 - 489
3X-RAY DIFFRACTION3chain CC30 - 489
4X-RAY DIFFRACTION4chain DD30 - 489

+
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