[English] 日本語
Yorodumi
- PDB-7jtj: Crystal structure of the second heterocyclization domain of yersi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jtj
TitleCrystal structure of the second heterocyclization domain of yersiniabactin synthetase
ComponentsIrp2 protein
KeywordsBIOSYNTHETIC PROTEIN / heterocyclization domain
Function / homology
Function and homology information


toxin biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain ...Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsXia, Y. / Gnann, A.D. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM123425-01 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: High-resolution structures of a siderophore-producing cyclization domain from Yersinia pestis offer a refined proposal of substrate binding.
Authors: Gnann, A.D. / Xia, Y. / Soule, J. / Barthelemy, C. / Mawani, J.S. / Musoke, S.N. / Castellano, B.M. / Brignole, E.J. / Frueh, D.P. / Dowling, D.P.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Irp2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9723
Polymers51,8291
Non-polymers1432
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-5 kcal/mol
Surface area18780 Å2
Unit cell
Length a, b, c (Å)89.290, 89.290, 140.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Irp2 protein / Ybt peptide synthetase HMWP2


Mass: 51828.766 Da / Num. of mol.: 1 / Fragment: heterocyclization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: irp2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z399
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.94→30.8 Å / Num. obs: 41892 / % possible obs: 98.9 % / Redundancy: 16.449 % / Biso Wilson estimate: 33.247 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Χ2: 0.915 / Net I/σ(I): 28.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.94-1.999.4180.6953.4129570.8480.73596.1
1.99-2.0513.5440.5525.3629940.9420.57399.4
2.05-2.1116.6860.4287.7828820.9680.44199.6
2.11-2.1717.0770.3489.7128490.980.35899.7
2.17-2.2517.2070.29911.2227500.9870.30799.6
2.25-2.3217.4330.23314.326270.9910.2499.2
2.32-2.4117.4530.20815.5725900.9930.21499.3
2.41-2.5117.5180.16518.8224300.9960.1798.4
2.51-2.6217.5880.14920.5323660.9960.15398.7
2.62-2.7517.540.1224.5522560.9970.12398.4
2.75-2.917.6490.09728.4921560.9990.198.6
2.9-3.0717.5830.08332.3220510.9990.08598.4
3.07-3.2917.5150.06741.0619300.9990.06998.9
3.29-3.5517.4250.05352.0318180.9990.05599.6
3.55-3.8917.1780.04364.39168210.04499.4
3.89-4.3517.1740.03872.48152610.0499.2
4.35-5.0217.2470.03180.43136710.03299.1
5.02-6.1517.2290.0378.4211770.9990.03199.2
6.15-8.716.7350.02883.893810.02999.8
8.7-30.813.9180.02687.354610.02796

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.15.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T7Z

5t7z


Resolution: 1.94→30.8 Å / SU ML: 0.1957 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.3598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2074 4.95 %Random selection
Rwork0.1799 39801 --
obs0.1817 41875 98.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.8 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 9 355 3783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763589
X-RAY DIFFRACTIONf_angle_d0.89094917
X-RAY DIFFRACTIONf_chiral_restr0.0822533
X-RAY DIFFRACTIONf_plane_restr0.0057648
X-RAY DIFFRACTIONf_dihedral_angle_d17.75331319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.30761320.24972525X-RAY DIFFRACTION95.85
1.99-2.040.25411350.22412602X-RAY DIFFRACTION99.2
2.04-2.090.23771370.2072624X-RAY DIFFRACTION99.53
2.09-2.160.24071380.18752641X-RAY DIFFRACTION99.75
2.16-2.230.23891370.19452635X-RAY DIFFRACTION99.64
2.23-2.310.24291370.1862619X-RAY DIFFRACTION99.21
2.31-2.40.24771370.18512628X-RAY DIFFRACTION99.28
2.4-2.510.23861370.1952628X-RAY DIFFRACTION98.61
2.51-2.640.22751370.22640X-RAY DIFFRACTION98.58
2.64-2.80.27681370.20322643X-RAY DIFFRACTION98.58
2.8-3.020.25631380.20522632X-RAY DIFFRACTION98.44
3.02-3.320.23041390.19222674X-RAY DIFFRACTION98.84
3.32-3.80.20321400.16272695X-RAY DIFFRACTION99.58
3.8-4.790.15931430.14092734X-RAY DIFFRACTION99.1
4.79-30.80.17791500.1662881X-RAY DIFFRACTION98.79
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)
10.743554883246-0.1988616822770.1736956376361.415622623320.1226609813951.149029454060.07652695498010.1361113652180.160071910814-0.190730914348-0.00371124533082-0.166512251654-0.1444420713490.0398499975164-0.06018337244970.3765471521990.002815832192510.06647299899880.1841020157550.05950791161380.288819556414-63.14319258764.178296786344.74384331063
21.89507941903-0.340958634984-0.9071037164431.149638663340.5530469345781.60520053671-0.03640392505990.0445482571340.0231867130127-0.147339587788-0.04119221838450.0161149319044-0.0988419446653-0.0632634892480.1065535926180.2681155102070.016824109598-0.01383591088530.11360954810.04321048902180.211789729582-66.44306476592.7266512093112.5692489588
30.798148682858-0.227085783824-0.05747728457681.617723094040.003456133681361.096742923060.03191009840850.1012358642090.0297736747531-0.2027811710430.0396406597703-0.0455284531267-0.03880522076630.0327765027829-0.05740970177930.19852073158-0.0264262904948-0.004967528324790.181852618610.01684469109970.141512377922-54.9665554812-14.60921859723.60119301807
43.60476666546-0.2903390612940.6870674469342.7296211973-1.33247424143.771273767670.06938006963240.281267732151-0.184653734228-0.383901551749-0.165203346013-0.4143946532150.08094610705930.8565072547270.08805288769730.257381490127-0.01644752234590.05413838568640.399049692201-0.02488116262460.227679814952-43.8788570647-17.6716084824-2.28954645602
51.92194359095-0.137127437128-0.3725916448491.159660617010.6875116008210.44886165839-0.1050976947810.09662566062290.0574252039143-0.1658810586860.0926070863415-0.0106359147004-0.4618754146510.551122324440.02352671492160.420631762391-0.0656416968491-0.007873260375060.2010627106480.07447633442470.276861752563-54.4773735989-7.34520311191.0392477725
60.9878449085490.0178715862345-0.7674546279581.073491185360.1995392602930.637598987760.02981087138360.0448888493628-0.027150561075-0.03060302402710.1357278860370.137285288111-0.122295375-0.174114830406-0.1764225169370.3137730940870.0160665910263-0.02309190531120.1628064543630.04182199458360.229884351993-64.148299131-14.57948172716.75181690055
72.006552425761.190648400840.8881927981533.27293797874-0.6224210490743.782428279850.1131158273620.0932671787497-0.0986211007172-0.032006640959-0.0380285407008-0.3120874556320.371151853490.232367070298-0.137746090420.2778641316960.019511808532-0.02224978168860.167864312153-0.03430040912020.217701792481-55.3769596191-29.24231782927.35742219131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1483:1532)
2X-RAY DIFFRACTION2(chain A and resid 1533:1680)
3X-RAY DIFFRACTION3(chain A and resid 1681:1772)
4X-RAY DIFFRACTION4(chain A and resid 1773:1802)
5X-RAY DIFFRACTION5(chain A and resid 1803:1847)
6X-RAY DIFFRACTION6(chain A and resid 1848:1886)
7X-RAY DIFFRACTION7(chain A and resid 1887:1910)

+
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