[English] 日本語
Yorodumi
- PDB-3wjz: Orotidine 5'-monophosphate decarboxylase D75N mutant from M. ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wjz
TitleOrotidine 5'-monophosphate decarboxylase D75N mutant from M. thermoautotrophicus complexed with 6-amino-UMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / protein-ligand complex / TIM barrel / decarboxylase / pyrimidine biosynthesis
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol
Similarity search - Function
: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel ...: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-AMINOURIDINE 5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.39 Å
AuthorsFujihashi, M. / Pai, E.F. / Miki, K.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.
Authors: Fujihashi, M. / Ishida, T. / Kuroda, S. / Kotra, L.P. / Pai, E.F. / Miki, K.
History
DepositionOct 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9375
Polymers27,3781
Non-polymers5594
Water3,135174
1
A: Orotidine 5'-phosphate decarboxylase
hetero molecules

A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,87510
Polymers54,7572
Non-polymers1,1188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5690 Å2
ΔGint-73 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.067, 103.595, 73.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

-
Components

#1: Protein Orotidine 5'-phosphate decarboxylase / OMP decarboxylase / OMPDCase / OMPdecase


Mass: 27378.418 Da / Num. of mol.: 1 / Mutation: D75N, L226R, N227I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: pyrF, MTH_129 / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-NUP / 6-AMINOURIDINE 5'-MONOPHOSPHATE


Mass: 339.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. DEPOSITORS SEQUENCED THE GENOME FROM M. THERMOAUTOTROPHICUS AND CONFIRMED IT IS PRO.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: Sodium citrate, pH 9, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.39→51.78 Å / Num. obs: 45280 / % possible obs: 100 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 39.8
Reflection shellResolution: 1.39→1.41 Å / Rmerge(I) obs: 0.307 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3WJY

3wjy


Resolution: 1.39→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.518 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17447 2259 5 %RANDOM
Rwork0.157 ---
obs0.1579 45007 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.15 Å2 / Biso mean: 17.4857 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 35 174 1839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221886
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9952569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5335253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73523.41582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17215328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3381519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0221450
X-RAY DIFFRACTIONr_mcbond_it0.7961.51188
X-RAY DIFFRACTIONr_mcangle_it1.44321930
X-RAY DIFFRACTIONr_scbond_it2.5933698
X-RAY DIFFRACTIONr_scangle_it4.3384.5637
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 158 -
Rwork0.183 3109 -
all-3267 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 18.6587 Å / Origin y: 40.4118 Å / Origin z: 29.8795 Å
111213212223313233
T0.0177 Å20.0008 Å2-0.0012 Å2-0.0136 Å2-0.0009 Å2--0.0092 Å2
L0.366 °2-0.0151 °20.0032 °2-0.5536 °2-0.0911 °2--0.2936 °2
S0.0045 Å °0.0304 Å °-0.0436 Å °-0.0768 Å °0.0096 Å °-0.0166 Å °0.0508 Å °-0.0017 Å °-0.0141 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 225
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION1A303 - 304
4X-RAY DIFFRACTION1A401 - 574

+
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