[English] 日本語
Yorodumi
- PDB-3v1p: Crystal structure of the mutant Q185A of orotidine 5'-monophospha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v1p
TitleCrystal structure of the mutant Q185A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / tim barrel / orotidine 5'-monophosphate decarboxylase / inhibitor BMP / LYASE / LYASE-LYASE INHIBITOR complex
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-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2012
Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Authors: Desai, B.J. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Goryanova, B. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Sep 13, 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
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5286
Polymers49,6552
Non-polymers8724
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-59 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.800, 63.862, 61.472
Angle α, β, γ (deg.)90.00, 115.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 24827.646 Da / Num. of mol.: 2 / Mutation: Q185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris HCl, 0.2M lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.37→41.928 Å / Num. all: 87599 / Num. obs: 87599 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTP

3ltp


Resolution: 1.37→41.928 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1784 4393 5.01 %RANDOM
Rwork0.1651 ---
all0.1658 87599 --
obs0.1658 87599 99.71 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.752 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4812 Å2-0 Å2-2.544 Å2
2--2.4231 Å2-0 Å2
3----0.9419 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 54 454 3823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063536
X-RAY DIFFRACTIONf_angle_d1.044802
X-RAY DIFFRACTIONf_dihedral_angle_d12.1071380
X-RAY DIFFRACTIONf_chiral_restr0.069541
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.38560.34871410.34582689X-RAY DIFFRACTION96
1.3856-1.40190.33941460.31882675X-RAY DIFFRACTION98
1.4019-1.4190.32381460.29642765X-RAY DIFFRACTION99
1.419-1.43690.26621560.26632727X-RAY DIFFRACTION100
1.4369-1.45580.29361580.26052781X-RAY DIFFRACTION100
1.4558-1.47580.25571380.23272762X-RAY DIFFRACTION100
1.4758-1.49690.24741330.21842789X-RAY DIFFRACTION100
1.4969-1.51920.23591340.20642765X-RAY DIFFRACTION100
1.5192-1.54290.25281450.20152772X-RAY DIFFRACTION100
1.5429-1.56820.21241460.1852780X-RAY DIFFRACTION100
1.5682-1.59530.17161390.17712781X-RAY DIFFRACTION100
1.5953-1.62430.20511520.16672775X-RAY DIFFRACTION100
1.6243-1.65550.18621270.16552772X-RAY DIFFRACTION100
1.6555-1.68930.19141380.1632763X-RAY DIFFRACTION100
1.6893-1.72610.18181480.15622790X-RAY DIFFRACTION100
1.7261-1.76620.16661630.15532751X-RAY DIFFRACTION100
1.7662-1.81040.1841520.15392796X-RAY DIFFRACTION100
1.8104-1.85930.17941380.15692788X-RAY DIFFRACTION100
1.8593-1.91410.18191600.15122738X-RAY DIFFRACTION100
1.9141-1.97580.16671570.15352773X-RAY DIFFRACTION100
1.9758-2.04640.17771460.15522773X-RAY DIFFRACTION100
2.0464-2.12840.18771580.16092771X-RAY DIFFRACTION100
2.1284-2.22520.15751380.15532803X-RAY DIFFRACTION100
2.2252-2.34260.16411390.15272773X-RAY DIFFRACTION100
2.3426-2.48930.19561720.1552767X-RAY DIFFRACTION100
2.4893-2.68150.17291450.16172822X-RAY DIFFRACTION100
2.6815-2.95130.1581490.16872786X-RAY DIFFRACTION100
2.9513-3.37820.14221210.1582826X-RAY DIFFRACTION100
3.3782-4.25550.14781400.13392820X-RAY DIFFRACTION100
4.2555-41.94720.16031680.15482833X-RAY DIFFRACTION99

+
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://pdbjlvh1.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