[English] 日本語
Yorodumi
- PDB-6m0a: The heme-bound structure of the chloroplast protein At3g03890 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m0a
TitleThe heme-bound structure of the chloroplast protein At3g03890
ComponentsAT3G03890 protein
KeywordsPLANT PROTEIN / heme binding protein
Function / homology
Function and homology information


heme catabolic process / chloroplast / heme binding / protein homodimerization activity
Similarity search - Function
Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel
Similarity search - Domain/homology
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / AT3G03890 protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, J. / Liu, L.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503703 China
National Natural Science Foundation of China (NSFC)31370759 China
CitationJournal: Biochem.J. / Year: 2020
Title: The Arabidopsis locus AT3G03890 encodes a dimeric beta-barrel protein implicated in heme degradation.
Authors: Wang, J. / Guo, Q. / Li, X. / Wang, X. / Liu, L.
History
DepositionFeb 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT3G03890 protein
B: AT3G03890 protein
C: AT3G03890 protein
D: AT3G03890 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,49212
Polymers127,8574
Non-polymers2,6348
Water4,900272
1
A: AT3G03890 protein
B: AT3G03890 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2466
Polymers63,9292
Non-polymers1,3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-55 kcal/mol
Surface area24160 Å2
MethodPISA
2
C: AT3G03890 protein
D: AT3G03890 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2466
Polymers63,9292
Non-polymers1,3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-56 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.346, 79.936, 80.105
Angle α, β, γ (deg.)99.950, 109.410, 104.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 69 through 70 and (name N...
21(chain B and ((resid 69 through 70 and (name N...
31(chain C and ((resid 69 through 70 and (name N...
41(chain D and (resid 69 through 95 or resid 97...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU(chain A and ((resid 69 through 70 and (name N...AA69 - 7040 - 41
12ASPASPHOHHOH(chain A and ((resid 69 through 70 and (name N...AA - M66 - 50137
13ASPASPHOHHOH(chain A and ((resid 69 through 70 and (name N...AA - M66 - 50137
21LYSLYSLEULEU(chain B and ((resid 69 through 70 and (name N...BB69 - 7040 - 41
22THRTHRHOHHOH(chain B and ((resid 69 through 70 and (name N...BB - N65 - 50136
23THRTHRHOHHOH(chain B and ((resid 69 through 70 and (name N...BB - N65 - 50136
31LYSLYSLEULEU(chain C and ((resid 69 through 70 and (name N...CC69 - 7040 - 41
32THRTHRHOHHOH(chain C and ((resid 69 through 70 and (name N...CC - O65 - 50136
33THRTHRHOHHOH(chain C and ((resid 69 through 70 and (name N...CC - O65 - 50136
41LYSLYSILEILE(chain D and (resid 69 through 95 or resid 97...DD69 - 9540 - 66
42GLYGLYGLYGLY(chain D and (resid 69 through 95 or resid 97...DD97 - 21268 - 183
43VALVALALAALA(chain D and (resid 69 through 95 or resid 97...DD213 - 214184 - 185
44VALVALHOHHOH(chain D and (resid 69 through 95 or resid 97...DD - P67 - 50138
45THRTHRTHRTHR(chain D and (resid 69 through 95 or resid 97...DD215186

-
Components

#1: Protein
AT3G03890 protein / FMN binding protein


Mass: 31964.373 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g03890, F20H23.6, F20H23_6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LDU1
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M trisodium citrate, 25% (w/v) PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60833 / % possible obs: 78.3 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.047 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5279 / CC1/2: 0.764 / Rpim(I) all: 0.345

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7R

4n7r


Resolution: 2.2→32.844 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.2329 2993 4.94 %
Rwork0.192 --
obs0.194 60639 90.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.06 Å2 / Biso mean: 56.9764 Å2 / Biso min: 24.16 Å2
Refinement stepCycle: final / Resolution: 2.2→32.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 184 272 8204
Biso mean--59.92 49.66 -
Num. residues----1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098124
X-RAY DIFFRACTIONf_angle_d0.9711054
X-RAY DIFFRACTIONf_chiral_restr0.0561236
X-RAY DIFFRACTIONf_plane_restr0.0051412
X-RAY DIFFRACTIONf_dihedral_angle_d16.4142955
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4658X-RAY DIFFRACTION10.708TORSIONAL
12B4658X-RAY DIFFRACTION10.708TORSIONAL
13C4658X-RAY DIFFRACTION10.708TORSIONAL
14D4658X-RAY DIFFRACTION10.708TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23610.28931090.2471218271
2.2361-2.27460.28981220.243256286
2.2746-2.3160.31581390.2392279593
2.316-2.36050.30671520.227287494
2.3605-2.40870.26761600.2208285095
2.4087-2.4610.28711330.2143286495
2.461-2.51820.28251630.2167288594
2.5182-2.58120.27131510.2169281994
2.5812-2.6510.26491620.205279093
2.651-2.72890.2471320.2156279092
2.7289-2.8170.30051300.2163267889
2.817-2.91760.30341360.2061248182
2.9176-3.03430.25121660.215289296
3.0343-3.17230.29721780.2164285795
3.1723-3.33940.23831360.2057288094
3.3394-3.54840.26371370.1999280393
3.5484-3.8220.23081130.1924278091
3.822-4.20590.18851500.1817249884
4.2059-4.81290.18011710.1517273792
4.8129-6.05750.19421400.1706289895
6.0575-32.8440.20031130.1727273190

+
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