[English] 日本語
Yorodumi
- PDB-4zl5: Crystal structure of the PmFTN variant E44H soaked in iron (45 min) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zl5
TitleCrystal structure of the PmFTN variant E44H soaked in iron (45 min)
ComponentsFerritin
KeywordsOXIDOREDUCTASE / ferritin / di-iron ferroxidase centre / 4-helix bundle
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / identical protein binding / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudo-nitzschia multiseries (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
Model details45 min soaked
AuthorsPfaffen, S. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Diatom Ferritin Optimized for Iron Oxidation but Not Iron Storage.
Authors: Pfaffen, S. / Bradley, J.M. / Abdulqadir, R. / Firme, M.R. / Moore, G.R. / Le Brun, N.E. / Murphy, M.E.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_keywords.pdbx_keywords

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,19130
Polymers113,8516
Non-polymers1,34024
Water12,592699
1
B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,765120
Polymers455,40424
Non-polymers5,36196
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area78240 Å2
ΔGint-1401 kcal/mol
Surface area136820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.460, 126.460, 170.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11E-204-

FE

21A-427-

HOH

31C-402-

HOH

41C-403-

HOH

51D-412-

HOH

61E-306-

HOH

71E-307-

HOH

-
Components

#1: Protein
Ferritin


Mass: 18975.146 Da / Num. of mol.: 6 / Mutation: E44H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudo-nitzschia multiseries (Diatom) / Gene: FTN / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B6DMH6, ferroxidase
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodiaum acetate pH 5.5, Ammonium sulfate, NaCl / Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Number: 789488 / Rsym value: 0.083 / D res high: 1.85 Å / D res low: 170.31 Å / Num. obs: 117178 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.8544.7110.0320.0328.9
4.145.8510.0570.0578.5
3.384.1410.060.068
2.933.3810.0630.0637.1
2.622.9310.0940.0946.7
2.392.6210.1360.1366.4
2.212.3910.1870.1876.2
2.072.2110.2770.2776.2
1.952.0710.470.476.2
1.851.9510.8090.8096.3
ReflectionResolution: 1.85→47.93 Å / Num. all: 117178 / Num. obs: 117178 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Rsym value: 0.083 / Net I/av σ(I): 6.578 / Net I/σ(I): 12 / Num. measured all: 789488
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.85-1.956.30.8090.9105995168100.3510.8092.199.2
1.95-2.076.20.471.699043158980.2070.473.599.1
2.07-2.216.20.2772.792854150470.1240.2775.699.4
2.21-2.396.20.1873.987303140810.0840.187899.7
2.39-2.626.40.1365.383469129890.060.13610.899.8
2.62-2.936.70.0947.378786118050.0410.09414.799.9
2.93-3.387.10.06310.174385105190.0270.06320.4100
3.38-4.1480.06107153889470.0230.0628100
4.14-5.858.50.0579.85994270260.0210.05730.7100
5.85-44.718.90.03217.83617340560.0120.03231.999.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREP11.1.03phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZKH

4zkh


Resolution: 1.85→47.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2028 / WRfactor Rwork: 0.1679 / FOM work R set: 0.8637 / SU B: 2.757 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1068 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 5867 5 %RANDOM
Rwork0.1722 ---
obs0.1739 111284 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.54 Å2 / Biso mean: 29.158 Å2 / Biso min: 6.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0 Å2
2--0.35 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.85→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7517 0 24 699 8240
Biso mean--36.2 34.79 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197865
X-RAY DIFFRACTIONr_bond_other_d0.0010.027192
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.93510740
X-RAY DIFFRACTIONr_angle_other_deg0.922316533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51625.481405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.913151275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4031537
X-RAY DIFFRACTIONr_chiral_restr0.1150.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029254
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021863
X-RAY DIFFRACTIONr_mcbond_it2.622.6043901
X-RAY DIFFRACTIONr_mcbond_other2.6162.6033900
X-RAY DIFFRACTIONr_mcangle_it3.5673.8784906
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 434 -
Rwork0.295 8090 -
all-8524 -
obs--99.09 %

+
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