[English] 日本語
Yorodumi
- PDB-3q98: Structure of ygeW encoded protein from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q98
TitleStructure of ygeW encoded protein from E. coli
Componentstranscarbamylase
KeywordsTRANSFERASE / Rossmann Fold / Unknown transcarbamylase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / carboxyl- or carbamoyltransferase activity / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / amino acid metabolic process / amino acid binding
Similarity search - Function
Putative carbamoyltransferase YgeW / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Knotted carbamoyltransferase YgeW / Putative carbamoyltransferase YgeW
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsLi, Y. / Jing, Z. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D.
CitationJournal: Proteins / Year: 2011
Title: The ygeW encoded protein from Escherichia coli is a knotted ancestral catabolic transcarbamylase.
Authors: Li, Y. / Jin, Z. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: transcarbamylase


Theoretical massNumber of molelcules
Total (without water)45,2281
Polymers45,2281
Non-polymers00
Water2,666148
1
A: transcarbamylase

A: transcarbamylase

A: transcarbamylase


Theoretical massNumber of molelcules
Total (without water)135,6843
Polymers135,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8280 Å2
ΔGint-38 kcal/mol
Surface area42940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.250, 78.250, 100.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein transcarbamylase


Mass: 45228.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygeW / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R7G1, UniProt: Q46803*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 200 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97933 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23528 / Num. obs: 23411 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1686 / % possible all: 96.1

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
SHELXmodel building
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→28.067 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8505 / SU ML: 0.23 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 3888 8.55 %RANDOM
Rwork0.1748 ---
all0.1799 49384 --
obs0.1791 22790 98.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.562 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 232.16 Å2 / Biso mean: 35.5349 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1--3.6883 Å20 Å20 Å2
2---3.6883 Å20 Å2
3---7.3766 Å2
Refinement stepCycle: LAST / Resolution: 2.001→28.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 0 148 3141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073049
X-RAY DIFFRACTIONf_angle_d1.0564115
X-RAY DIFFRACTIONf_chiral_restr0.072454
X-RAY DIFFRACTIONf_plane_restr0.005530
X-RAY DIFFRACTIONf_dihedral_angle_d16.5011126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0007-2.07220.2393910.20243989438095
2.0722-2.15520.2253830.18454152453598
2.1552-2.25320.24493810.18134161454298
2.2532-2.3720.24813950.17794193458898
2.372-2.52050.24263840.18394146453098
2.5205-2.71490.24583950.17994183457899
2.7149-2.98790.27693890.19034181457099
2.9879-3.41960.21443940.18154190458499
3.4196-4.30580.18863830.14674202458599
4.3058-28.06970.21273930.174211460499
Refinement TLS params.Method: refined / Origin x: 23.0719 Å / Origin y: 49.4722 Å / Origin z: 46.1146 Å
111213212223313233
T0.1303 Å2-0.017 Å2-0.007 Å2-0.124 Å20.001 Å2--0.1266 Å2
L1.6904 °2-0.0909 °2-0.3883 °2-1.0475 °20.2113 °2--0.8804 °2
S0.0619 Å °0.1222 Å °0.0639 Å °-0.128 Å °-0.0202 Å °-0.1455 Å °-0.0594 Å °0.0453 Å °-0.0424 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 396
2X-RAY DIFFRACTION1allA1 - 544

+
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