[English] 日本語
Yorodumi
- PDB-6vna: Pden_1323 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vna
TitlePden_1323
ComponentsPyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
KeywordsMETAL BINDING PROTEIN / Heme
Function / homologyHeme utilization protein HutZ / FMN-binding split barrel / Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
Function and homology information
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIsiorho, E.A. / Mansoorabadi, S.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A noncanonical heme oxygenase specific for the degradation of c-type heme.
Authors: Li, S. / Isiorho, E.A. / Owens, V.L. / Donnan, P.H. / Odili, C.L. / Mansoorabadi, S.O.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: 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: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
C: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)52,1073
Polymers52,1073
Non-polymers00
Water84747
1
A: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
C: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)34,7382
Polymers34,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-21 kcal/mol
Surface area13190 Å2
MethodPISA
2
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein

B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)34,7382
Polymers34,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.843, 117.044, 59.382
Angle α, β, γ (deg.)90.000, 99.376, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Mass: 17368.971 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_1323, Pden_1574 / Production host: Escherichia coli (E. coli) / References: UniProt: A1B1N4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: glycerol, PEG 4000, sodium acetate, Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→61.25 Å / Num. obs: 32977 / % possible obs: 99.7 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1677 / CC1/2: 0.582

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: itasser

Resolution: 2.2→58.657 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2587 1294 5.215 %
Rwork0.2115 --
all0.214 --
obs-24814 99.595 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.131 Å2
Baniso -1Baniso -2Baniso -3
1--2.995 Å20 Å2-3.54 Å2
2---3.766 Å20 Å2
3---7.519 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 47 3197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133210
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173187
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6434360
X-RAY DIFFRACTIONr_angle_other_deg2.3461.5787305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.86919.07172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5461540
X-RAY DIFFRACTIONr_chiral_restr0.0590.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023615
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02701
X-RAY DIFFRACTIONr_nbd_refined0.2030.2509
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.22683
X-RAY DIFFRACTIONr_nbtor_refined0.1430.21431
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0720.29
X-RAY DIFFRACTIONr_nbd_other0.2190.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.23
X-RAY DIFFRACTIONr_mcbond_it5.0536.4691671
X-RAY DIFFRACTIONr_mcbond_other5.0466.4681670
X-RAY DIFFRACTIONr_mcangle_it7.3889.682077
X-RAY DIFFRACTIONr_mcangle_other7.3899.6822078
X-RAY DIFFRACTIONr_scbond_it5.327.2661538
X-RAY DIFFRACTIONr_scbond_other5.3197.2691539
X-RAY DIFFRACTIONr_scangle_it8.34710.6452282
X-RAY DIFFRACTIONr_scangle_other8.34610.6472283
X-RAY DIFFRACTIONr_lrange_it11.32375.8613140
X-RAY DIFFRACTIONr_lrange_other11.32775.8623135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.4151080.3761677X-RAY DIFFRACTION98.892
2.257-2.3190.324850.3731695X-RAY DIFFRACTION99.4969
2.319-2.3860.403980.3461637X-RAY DIFFRACTION99.1995
2.386-2.4590.369820.3241607X-RAY DIFFRACTION99.5286
2.459-2.540.284940.2991539X-RAY DIFFRACTION99.4519
2.54-2.6290.321700.2771500X-RAY DIFFRACTION99.6193
2.629-2.7280.315730.2421450X-RAY DIFFRACTION99.5425
2.728-2.8390.303650.2291390X-RAY DIFFRACTION99.7942
2.839-2.9650.3660.2161362X-RAY DIFFRACTION99.7904
2.965-3.1090.249750.1931267X-RAY DIFFRACTION99.7028
3.109-3.2770.309760.1981223X-RAY DIFFRACTION99.7696
3.277-3.4750.208660.1771145X-RAY DIFFRACTION99.8351
3.475-3.7140.235710.1891060X-RAY DIFFRACTION99.9117
3.714-4.010.262550.1911014X-RAY DIFFRACTION99.9065
4.01-4.3910.183450.157938X-RAY DIFFRACTION99.8984
4.391-4.9070.195390.163858X-RAY DIFFRACTION99.8886
4.907-5.660.265480.189733X-RAY DIFFRACTION99.8721
5.66-6.9170.227340.224642X-RAY DIFFRACTION100
6.917-9.720.272230.208502X-RAY DIFFRACTION100
9.72-58.6570.234210.226281X-RAY DIFFRACTION99.67

+
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