[English] 日本語
Yorodumi
- PDB-5xao: Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xao
TitleCrystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / Fructosyl peptide oxidase / FAD
Function / homology
Function and homology information


saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding
Similarity search - Function
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
ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / FAD dependent oxidoreductase domain-containing protein
Similarity search - Component
Biological speciesPhaeosphaeria nodorum
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYoshida, H. / Kamitori, S. / Sode, K.
Citation
Journal: Sci Rep / Year: 2017
Title: X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction
Authors: Shimasaki, T. / Yoshida, H. / Kamitori, S. / Sode, K.
#1: Journal: Biotechnol. Bioeng. / Year: 2010
Title: Motif-based search for a novel fructosyl peptide oxidase from genome databases.
Authors: Kim, S. / Ferri, S. / Tsugawa, W. / Mori, K. / Sode, K.
History
DepositionMar 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,07515
Polymers98,1152
Non-polymers1,96013
Water13,745763
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0558
Polymers49,0581
Non-polymers9987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-23 kcal/mol
Surface area17450 Å2
MethodPISA
2
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0207
Polymers49,0581
Non-polymers9626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-11 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.119, 109.065, 95.017
Angle α, β, γ (deg.)90.000, 98.830, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AC

#1: Protein Uncharacterized protein


Mass: 49057.516 Da / Num. of mol.: 2 / Fragment: UNP residues 1-431 / Mutation: N56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (fungus)
Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: SNOG_08398 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0UIL6

-
Non-polymers , 5 types, 776 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Tacsimate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.64 Å / Num. obs: 80576 / % possible obs: 96 % / Redundancy: 3.58 % / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.08 / Χ2: 0.97 / Net I/σ(I): 6.6 / Num. measured all: 290996 / Scaling rejects: 2183
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsΧ2Diffraction-ID% possible all
1.8-1.863.540.5141.81.17193.3
1.86-1.943.530.45821.15193.8
1.94-2.033.510.3932.41.16194.3
2.03-2.133.490.3292.71.09194.9
2.13-2.273.480.263.21.01195.2
2.27-2.443.530.20440.96196.6
2.44-2.693.620.1525.20.9196.9
2.69-3.073.720.0957.80.82197.8
3.07-3.873.710.0515.10.75198.4
3.87-19.643.70.04119.30.73199.1

-
Processing

Software
NameVersionClassification
CrystalCleardata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
d*TREKdata scaling
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T1F

5t1f


Resolution: 1.8→19.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.062 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.155
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 4016 5 %RANDOM
Rwork0.2092 ---
obs0.212 76559 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.36 Å2 / Biso mean: 32.891 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.8→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 123 763 7546
Biso mean--27.57 37.67 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0196965
X-RAY DIFFRACTIONr_bond_other_d00.026496
X-RAY DIFFRACTIONr_angle_refined_deg0.8581.9639471
X-RAY DIFFRACTIONr_angle_other_deg0.527314947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3795862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33323.77305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.612151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021541
X-RAY DIFFRACTIONr_chiral_restr0.0560.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217902
X-RAY DIFFRACTIONr_gen_planes_other00.021619
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 277 -
Rwork0.355 5448 -
all-5725 -
obs--93.53 %

+
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