[English] 日本語
Yorodumi
- PDB-1r1n: Tri-nuclear oxo-iron clusters in the ferric binding protein from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r1n
TitleTri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae
ComponentsFerric-iron Binding Protein
KeywordsIRON BINDING PROTEIN
Function / homology
Function and homology information


iron ion transport / transmembrane transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OXO-IRON CLUSTER 2 / OXO-IRON CLUSTER 1 / OXO-IRON CLUSTER 3 / Major ferric iron-binding protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhu, H. / Alexeev, D. / Hunter, D.J. / Campopiano, D.J. / Sadler, P.J.
CitationJournal: Biochem.J. / Year: 2003
Title: Oxo-iron clusters in a bacterial iron-trafficking protein: new roles for a conserved motif.
Authors: Zhu, H. / Alexeev, D. / Hunter, D.J. / Campopiano, D.J. / Sadler, P.J.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif / struct_site
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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / pdbx_distant_solvent_atoms ...chem_comp_atom / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _chem_comp_atom.pdbx_stereo_config

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferric-iron Binding Protein
B: Ferric-iron Binding Protein
C: Ferric-iron Binding Protein
D: Ferric-iron Binding Protein
E: Ferric-iron Binding Protein
F: Ferric-iron Binding Protein
G: Ferric-iron Binding Protein
H: Ferric-iron Binding Protein
I: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,44418
Polymers303,1959
Non-polymers3,2499
Water50,7482817
1
A: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.500, 146.500, 114.969
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Ferric-iron Binding Protein


Mass: 33688.348 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Neisseria gonorrhoeae (bacteria) / References: UniProt: P17259
#2: Chemical
ChemComp-CNB / OXO-IRON CLUSTER 1


Mass: 351.592 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3H8O11
#3: Chemical
ChemComp-CN1 / OXO-IRON CLUSTER 2


Mass: 368.599 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3H9O12
#4: Chemical ChemComp-CNF / OXO-IRON CLUSTER 3


Mass: 368.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3H9O12
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2817 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 1450, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: multilayer osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. all: 283046 / Num. obs: 280085 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 7.1
Reflection shellResolution: 1.74→1.82 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / Num. unique all: 33430 / Rsym value: 0.47 / % possible all: 87.1

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O7T

1o7t


Resolution: 1.74→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 11189 -RANDOM
Rwork0.167 ---
all0.167 283046 --
obs0.167 280085 99 %-
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 1.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21402 0 131 2817 24350
LS refinement shellResolution: 1.74→1.82 Å
RfactorNum. reflection% reflection
Rfree0.38 1366 -
Rwork0.34 --
obs-33430 87.1 %

+
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