[English] 日本語
Yorodumi
- PDB-3ljp: Crystal structure of choline oxidase V464A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ljp
TitleCrystal structure of choline oxidase V464A mutant
ComponentsCholine oxidase
KeywordsOXIDOREDUCTASE / Flavoenzyme Oxidase / Covalently linked FAD / FAD / Flavoprotein
Function / homology
Function and homology information


choline oxidase / choline:oxygen 1-oxidoreductase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding
Similarity search - Function
Arc Repressor Mutant - #110 / Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Arc Repressor Mutant / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase ...Arc Repressor Mutant - #110 / Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Arc Repressor Mutant / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Choline oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFinnegan, S. / Agniswamy, J. / Weber, I.T. / Giovanni, G.
CitationJournal: Biochemistry / Year: 2010
Title: Role of valine 464 in the flavin oxidation reaction catalyzed by choline oxidase.
Authors: Finnegan, S. / Agniswamy, J. / Weber, I.T. / Gadda, G.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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: Choline oxidase
B: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3174
Polymers119,7412
Non-polymers1,5752
Water8,503472
1
A: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6582
Polymers59,8711
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6582
Polymers59,8711
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.040, 87.040, 353.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Choline oxidase /


Mass: 59870.707 Da / Num. of mol.: 2 / Mutation: V464A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: codA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q7X2H8, choline oxidase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10-15% PEG 6000, 50-200mM magnesium acetate, 200mM trimethylamine, 0.08M sodium cacodilate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 70579 / Num. obs: 67756 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.31
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 5.51 / Num. unique all: 6854 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBV

2jbv


Resolution: 2.2→43.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.196 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22673 3213 5.1 %RANDOM
Rwork0.1649 ---
all0.168 67756 --
obs0.16797 60393 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.429 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8194 0 106 472 8772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0218510
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.96711606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88751058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09423.627408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.902151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0921576
X-RAY DIFFRACTIONr_chiral_restr0.180.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216668
X-RAY DIFFRACTIONr_mcbond_it1.1341.55280
X-RAY DIFFRACTIONr_mcangle_it1.9928514
X-RAY DIFFRACTIONr_scbond_it3.63333230
X-RAY DIFFRACTIONr_scangle_it5.6324.53092
LS refinement shellResolution: 2.196→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 215 -
Rwork0.152 4128 -
obs--89.03 %
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)
10.362-0.1429-0.03630.37220.09940.49190.0009-0.01540.00510.00610.0252-0.0195-0.00120.052-0.02620.0114-0.00440.01260.0081-0.00620.063140.491-7.167-35.892
20.3619-0.2121-0.20660.47280.11080.61170.01710.00560.0216-0.0188-0.0045-0.0279-0.0334-0.0083-0.01270.0042-0.00040.00950.0006-0.00310.048438.017-2.868-75.116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 527
2X-RAY DIFFRACTION2B1 - 527

+
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