[English] 日本語
Yorodumi
- PDB-5x3d: Crystal structure of HEP-CMP-bound form of cytidylyltransferase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x3d
TitleCrystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis
ComponentsPhosphoenolpyruvate phosphomutase
KeywordsTRANSFERASE / Cytidylyltransferase / Nucleotidyltransferase / fosfomycin biosynthesis
Function / homology
Function and homology information


2-hydroxyethylphosphonate cytidylyltransferase / phosphoenolpyruvate mutase / phosphoenolpyruvate mutase activity / antibiotic biosynthetic process / nucleotidyltransferase activity
Similarity search - Function
Phosphoenolpyruvate phosphomutase, core / : / Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-7XL / Fosfomycin biosynthesis bifunctional protein Fom1
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsTomita, T. / Cho, S.H. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme
Authors: Cho, S.H. / Kim, S.Y. / Tomita, T. / Shiraishi, T. / Park, J.S. / Sato, S. / Kudo, F. / Eguchi, T. / Funa, N. / Nishiyama, M. / Kuzuyama, T.
History
DepositionFeb 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2492
Polymers17,8171
Non-polymers4311
Water1,31573
1
A: Phosphoenolpyruvate phosphomutase
hetero molecules

A: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4974
Polymers35,6352
Non-polymers8622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area1430 Å2
ΔGint-12 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.909, 71.909, 109.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Phosphoenolpyruvate phosphomutase / Fom1


Mass: 17817.314 Da / Num. of mol.: 1 / Fragment: Cytidylyltransferase domain, UNP residues 1-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wedmorensis (bacteria) / Gene: Fom1(N) / Plasmid: pHis8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P96074
#2: Chemical ChemComp-7XL / [[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid


Mass: 431.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 4.3 M sodium chloride

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97908, 0.97927, 0.96404
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.979271
30.964041
ReflectionResolution: 1.93→50 Å / Num. obs: 13233 / % possible obs: 99.9 % / Redundancy: 20.9 % / Net I/σ(I): 63.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.93→30.05 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.993 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23376 649 4.9 %RANDOM
Rwork0.19111 ---
obs0.19307 12523 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.472 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.93→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 27 73 1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191043
X-RAY DIFFRACTIONr_bond_other_d0.0040.021008
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.991424
X-RAY DIFFRACTIONr_angle_other_deg1.0713.0082309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10322.82646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15415170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6891510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211148
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4013.175503
X-RAY DIFFRACTIONr_mcbond_other2.3793.167502
X-RAY DIFFRACTIONr_mcangle_it3.2624.736627
X-RAY DIFFRACTIONr_mcangle_other3.2614.745628
X-RAY DIFFRACTIONr_scbond_it3.3193.587540
X-RAY DIFFRACTIONr_scbond_other3.3183.587540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0015.228798
X-RAY DIFFRACTIONr_long_range_B_refined6.31626.1281213
X-RAY DIFFRACTIONr_long_range_B_other6.22725.9391192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 57 -
Rwork0.226 876 -
obs--100 %

+
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