[English] 日本語
Yorodumi
- PDB-1g2a: THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WIT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g2a
TitleTHE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN
ComponentsPOLYPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / actinonin / inhibition / Polypeptide deformylase
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACTINONIN / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsClements, J.M. / Beckett, P. / Brown, A. / Catlin, C. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Baker, P.J. / Rodgers, H.F. ...Clements, J.M. / Beckett, P. / Brown, A. / Catlin, C. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Baker, P.J. / Rodgers, H.F. / Barynin, V. / Rice, D.W. / Hunter, M.G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2001
Title: Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor.
Authors: Clements, J.M. / Beckett, R.P. / Brown, A. / Catlin, G. / Lobell, M. / Palan, S. / Thomas, W. / Whittaker, M. / Wood, S. / Salama, S. / Baker, P.J. / Rodgers, H.F. / Barynin, V. / Rice, D.W. / Hunter, M.G.
History
DepositionOct 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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_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: POLYPEPTIDE DEFORMYLASE
B: POLYPEPTIDE DEFORMYLASE
C: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0119
Polymers57,6793
Non-polymers1,3336
Water13,061725
1
A: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6703
Polymers19,2261
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6703
Polymers19,2261
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: POLYPEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6703
Polymers19,2261
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.700, 63.100, 85.600
Angle α, β, γ (deg.)90.00, 121.40, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

-
Components

#1: Protein POLYPEPTIDE DEFORMYLASE / E.C.3.5.1.31 / N-FORMYLMETHIONYLAMINOACYL-TRNA DEFORMYLASE / PDF / FMS


Mass: 19226.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DEF / Plasmid: PET24-PDF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6K3, EC: 3.5.1.31
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE


Mass: 385.498 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mg/ml PDF, 20mM actinonin, 50mM HEPES, pH 7.5 + 25-32% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMinhibitor1drop
350 mMHEPES1drop
425-32 %PEG40001reservoir
50.1 Msodium citrate1reservoir
60.2 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 28, 1999 / Details: MSC Yale Mirrors
RadiationMonochromator: msc yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→14 Å / Num. all: 62907 / Num. obs: 54729 / % possible obs: 0.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.6
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.191 / % possible all: 86.8
Reflection
*PLUS
% possible obs: 85.9 %
Reflection shell
*PLUS
% possible obs: 86.8 % / Num. unique obs: 3634 / Mean I/σ(I) obs: 3.9

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2736 5 %random
Rwork0.19 ---
all0.191 54729 --
obs0.191 54729 --
Refinement stepCycle: LAST / Resolution: 1.75→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 92 725 4764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.027
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.437

+
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