[English] 日本語
Yorodumi
- PDB-3bhf: Crystal structure of R49K mutant of Monomeric Sarcosine Oxidase c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bhf
TitleCrystal structure of R49K mutant of Monomeric Sarcosine Oxidase crystallized in PEG as precipitant
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / Cytoplasm / FAD
Function / homology
Function and homology information


sarcosine oxidase (formaldehyde-forming) / L-lysine catabolic process to acetyl-CoA via L-pipecolate / L-pipecolate oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / peroxisome / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHassan-Abdallah, A. / Zhao, G. / Chen, Z. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2008
Title: Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: a context-sensitive model for the electrostatic impact of arginine to lysine mutations.
Authors: Hassan-Abdallah, A. / Zhao, G. / Chen, Z.W. / Mathews, F.S. / Schuman Jorns, M.
#1: Journal: Structure / Year: 1999
Title: Monomeric Sarcosine Oxidase: Structure of a Covalently Flavinylated amine Oxidizing Enzyme
Authors: Trickey, P. / Wagner, M.A. / Jorns, M.S. / Mathews, F.S.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monomeric sarcosine oxidase
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0516
Polymers86,4092
Non-polymers1,6424
Water6,305350
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0263
Polymers43,2051
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0263
Polymers43,2051
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.348, 70.456, 79.595
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Monomeric sarcosine oxidase / MSOX


Mass: 43204.535 Da / Num. of mol.: 2 / Mutation: R49K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: soxA, sox / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 200 mM NaNO3, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 46999 / Num. obs: 43803 / % possible obs: 93.2 % / Observed criterion σ(F): -0.9 / Observed criterion σ(I): -0.9 / Redundancy: 3.5 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2 / Num. unique all: 3448 / % possible all: 74

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9F

1l9f
PDB Unreleased entry


Resolution: 2.1→39.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 179408.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2109 5 %RANDOM
Rwork0.202 ---
obs0.202 42142 90.4 %-
Displacement parametersBiso mean: 37.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 108 350 6434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 276 5 %
Rwork0.332 5233 -
obs-5468 71.3 %

+
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