[English] 日本語
Yorodumi
- PDB-5hjf: The apo form of Dps4 from Nostoc punctiforme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hjf
TitleThe apo form of Dps4 from Nostoc punctiforme
ComponentsFerritin, Dps family protein
KeywordsMETAL BINDING PROTEIN / ferredoxin / oxidative stress
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding
Similarity search - Function
Dps protein family signature 2. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ferritin, Dps family protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsHowe, C. / Moparthi, V.K. / Persson, K. / Stensjo, K.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Energy Agency11674-5 Sweden
CitationJournal: To Be Published
Title: On the trail of iron and zinc bindning to Dps4 from N. punctiforme
Authors: Howe, C. / Moparthi, V.K. / Persson, K. / Stensjo, K.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein


Theoretical massNumber of molelcules
Total (without water)83,7934
Polymers83,7934
Non-polymers00
Water12,304683
1
A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein

A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein

A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein


Theoretical massNumber of molelcules
Total (without water)251,38012
Polymers251,38012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area66020 Å2
ΔGint-309 kcal/mol
Surface area63550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.884, 101.884, 146.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-236-

HOH

21B-284-

HOH

31B-293-

HOH

41B-355-

HOH

51D-205-

HOH

61D-312-

HOH

-
Components

#1: Protein
Ferritin, Dps family protein / / DNA binding protein from starved cells (Dps)


Mass: 20948.359 Da / Num. of mol.: 4 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R5799 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2J981
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.61 Å3/Da / Density % sol: 52.93 % / Description: Long rod-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% SOKALAN HP 66, 0.1 M HEPES pH 7.0 and 0.2 M NaOAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984002 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984002 Å / Relative weight: 1
ReflectionResolution: 1.59→48.75 Å / Num. obs: 115112 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 18.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.6 / Num. measured all: 1174206 / Scaling rejects: 56
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
1.59-1.6410.20.5073.8113526111300.92198.5
6.15-48.759.90.05448.42029820500.99899.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.14data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→48.107 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1462 4654 4.04 %Shells
Rwork0.1301 110420 --
obs0.1308 115074 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.08 Å2 / Biso mean: 23.258 Å2 / Biso min: 11.99 Å2
Refinement stepCycle: final / Resolution: 1.59→48.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 0 683 6452
Biso mean---32.32 -
Num. residues----722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095974
X-RAY DIFFRACTIONf_angle_d1.178121
X-RAY DIFFRACTIONf_chiral_restr0.046899
X-RAY DIFFRACTIONf_plane_restr0.0071072
X-RAY DIFFRACTIONf_dihedral_angle_d14.4642179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5887-1.60680.324410.1734367397
1.6068-1.62570.1577381899
1.6257-1.64550.14913837100
1.6455-1.66640.18014920.14143327100
1.6664-1.68830.14063790100
1.6883-1.71140.13693865100
1.7114-1.73590.1724560.13843333100
1.7359-1.76180.13953874100
1.7618-1.78930.16584170.13773394100
1.7893-1.81860.13463875100
1.8186-1.850.14243776100
1.85-1.88360.16944040.14143423100
1.8836-1.91990.14553867100
1.9199-1.95910.16893580.13663499100
1.9591-2.00170.13183789100
2.0017-2.04820.14673320.13033509100
2.0482-2.09940.12443825100
2.0994-2.15620.13923060.11973523100
2.1562-2.21970.12413870100
2.2197-2.29130.15432770.12253553100
2.2913-2.37320.11973868100
2.3732-2.46820.14722220.1213598100
2.4682-2.58050.13522320.11793621100
2.5805-2.71660.15152140.12393626100
2.7166-2.88670.14521660.1293691100
2.8867-3.10960.14851470.13453716100
3.1096-3.42250.14751400.13493710100
3.4225-3.91750.15041490.13123733100
3.9175-4.93492013660100
4.93491403777100
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)
10.47170.1183-0.34380.2853-0.13350.58190.01010.0465-0.05260.0208-0.0114-0.00960.0802-0.02140.00470.17630.01170.0210.1356-0.00090.16482.696630.3545-13.2288
20.5410.2715-0.36010.4235-0.24590.8668-0.01710.0203-0.0727-0.0013-0.02960.01960.067-0.07610.04290.1487-0.0165-0.00110.1649-0.01560.1556-15.472440.8586-20.8934
30.42660.21340.14210.79350.25260.4836-0.01020.01-0.0340.0258-0.0118-0.02150.09430.10780.02170.14330.04260.00380.18810.02880.172424.504840.96038.8026
40.43140.24190.20630.50570.15120.5401-0.0268-0.0159-0.02820.05880.0122-0.00490.07040.04480.02630.13380.0150.00460.13270.0250.124810.783142.578925.3562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 182
2X-RAY DIFFRACTION2chain BB4 - 182
3X-RAY DIFFRACTION3chain CC4 - 182
4X-RAY DIFFRACTION4chain DD-2 - 182

+
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