[English] 日本語
Yorodumi
- PDB-9h64: Crystal structure of Thermoanaerobacterales bacterium monoamine o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h64
TitleCrystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with n-heptylamine
ComponentsMonoamine oxidase
KeywordsFLAVOPROTEIN / monoamine oxidase / Thermoanaerobacterales bacterium / enzyme / n-heptylamine
Function / homology: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / : / FLAVIN-ADENINE DINUCLEOTIDE / Monoamine oxidase
Function and homology information
Biological speciesThermoanaerobacterales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBasile, L. / Poli, C. / Santema, L.L. / Lesenciuc, R.C. / Fraaije, M.W. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationMUR PNRR NODES Italy
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Altering substrate specificity of a thermostable bacterial monoamine oxidase by structure-based mutagenesis.
Authors: Basile, L. / Poli, C. / Santema, L.L. / Lesenciuc, R.C. / Fraaije, M.W. / Binda, C.
History
DepositionOct 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monoamine oxidase
B: Monoamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0057
Polymers100,1802
Non-polymers1,8265
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-21 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.972, 103.690, 120.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Monoamine oxidase


Mass: 50089.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterales bacterium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0AAJ6N6J2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1ISO / n-heptylamine / heptan-1-amine


Mass: 115.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG4000, 100 mM TRIS/HCl buffer pH 8.5, 200 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965459 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.6→39.36 Å / Num. obs: 110383 / % possible obs: 96.7 % / Redundancy: 3.6 % / CC1/2: 0.942 / Net I/σ(I): 14.1
Reflection shellResolution: 1.6→1.642 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5536 / CC1/2: 0.713

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.36 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.426 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22611 5487 5 %RANDOM
Rwork0.19455 ---
obs0.19608 104549 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.17 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.6→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 123 597 7420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137000
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176476
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6689598
X-RAY DIFFRACTIONr_angle_other_deg1.4821.58614838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.00920.372376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82115950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1681570
X-RAY DIFFRACTIONr_chiral_restr0.0780.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021600
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_it1.3681.6133582
X-RAY DIFFRACTIONr_mcbond_other1.3571.6113580
X-RAY DIFFRACTIONr_mcangle_it1.9822.4194474
X-RAY DIFFRACTIONr_mcangle_other1.9742.4184474
X-RAY DIFFRACTIONr_scbond_it2.1181.8243418
X-RAY DIFFRACTIONr_scbond_other2.1171.8243419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2122.6515125
X-RAY DIFFRACTIONr_long_range_B_refined4.0519.5467969
X-RAY DIFFRACTIONr_long_range_B_other3.98319.2467821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14064 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 448 -
Rwork0.24 7883 -
obs--99.13 %

+
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://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