[English] 日本語
Yorodumi
- PDB-1ji4: NAP protein from helicobacter pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ji4
TitleNAP protein from helicobacter pylori
ComponentsNEUTROPHIL-ACTIVATING PROTEIN A
KeywordsMETAL TRANSPORT / dodecamer / four-helix bundle
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / 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 ...Dps protein family signature 2. / Dps protein family signature 1. / 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
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsZanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Structure of the Neutrophil-activating Protein from Helicobacter pylori
Authors: Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron Binding Site
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionJun 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_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 / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUTROPHIL-ACTIVATING PROTEIN A
B: NEUTROPHIL-ACTIVATING PROTEIN A
C: NEUTROPHIL-ACTIVATING PROTEIN A
D: NEUTROPHIL-ACTIVATING PROTEIN A
E: NEUTROPHIL-ACTIVATING PROTEIN A
F: NEUTROPHIL-ACTIVATING PROTEIN A
G: NEUTROPHIL-ACTIVATING PROTEIN A
H: NEUTROPHIL-ACTIVATING PROTEIN A
I: NEUTROPHIL-ACTIVATING PROTEIN A
J: NEUTROPHIL-ACTIVATING PROTEIN A
K: NEUTROPHIL-ACTIVATING PROTEIN A
L: NEUTROPHIL-ACTIVATING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,61348
Polymers203,52512
Non-polymers2,08836
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39070 Å2
ΔGint-519 kcal/mol
Surface area63670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.778, 133.225, 95.228
Angle α, β, γ (deg.)90.00, 93.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
NEUTROPHIL-ACTIVATING PROTEIN A / NAP A / BACTERIOFERRITIN


Mass: 16960.396 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: NAPA / Production host: Bacillus subtilis (bacteria) / References: UniProt: P43313
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium acetate, citrate buffer, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium acetate1reservoir
20.1 Mcitrate1reservoirpH5.6
330 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.3 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 2000
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 71729 / Num. obs: 71729 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 5.9 / Num. unique all: 9698 / % possible all: 90.9
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.52 Å / % possible obs: 90.9 % / Num. unique obs: 9698 / Rmerge(I) obs: 0.087

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 2.52→20.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1727967.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: Only one monomer was treated independently and all the others were generated from the transformation matrices according to the Strict-ncs of CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7263 10.1 %RANDOM
Rwork0.215 ---
all-71706 --
obs-71706 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å24.86 Å2
2---5.07 Å20 Å2
3---7.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.52→20.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14352 0 24 742 15118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d1.41
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 997 10.3 %
Rwork0.278 8692 -
obs-9698 76.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4MPD.PARAM
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.278

+
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