[English] 日本語
Yorodumi
- PDB-3pbw: Crystal structure of the mutant L123N of orotidine 5'-monophospha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pbw
TitleCrystal structure of the mutant L123N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
ComponentsOrotidine 5'-monophosphate decarboxylase
KeywordsLYASE / tim barrel / orotidine 5'-monophosphate decarboxylase / 6-azauridine 5'-monophosphate
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-AZA URIDINE 5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanobacterium thermoautotrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Iiams, V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2011
Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Authors: Iiams, V. / Desai, B.J. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 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'-monophosphate decarboxylase
B: Orotidine 5'-monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7712
Non-polymers6502
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-40 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.785, 64.140, 61.610
Angle α, β, γ (deg.)90.00, 115.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 24885.643 Da / Num. of mol.: 2 / Mutation: R101P, L123N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobacterium thermoautotrophicum (archaea)
Strain: Delta H / Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-UP6 / 6-AZA URIDINE 5'-MONOPHOSPHATE / 6-AZA-UMP


Mass: 325.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N3O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.1M Bis-Tris , 0.2M lithium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.3→32.358 Å / Num. all: 101238 / Num. obs: 101238 / % possible obs: 98.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G18

3g18


Resolution: 1.3→32.358 Å / SU ML: 0.14 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 5061 5 %RANDOM
Rwork0.1613 ---
all0.162 101238 --
obs0.162 101238 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.318 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2687 Å2-0 Å2-1.4713 Å2
2--2.7049 Å2-0 Å2
3----0.4362 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 42 482 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063572
X-RAY DIFFRACTIONf_angle_d1.1224853
X-RAY DIFFRACTIONf_dihedral_angle_d15.9681387
X-RAY DIFFRACTIONf_chiral_restr0.072548
X-RAY DIFFRACTIONf_plane_restr0.007649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.21461570.20043042X-RAY DIFFRACTION94
1.3148-1.33030.20451760.19983156X-RAY DIFFRACTION97
1.3303-1.34650.21631570.19343156X-RAY DIFFRACTION97
1.3465-1.36350.19481600.193137X-RAY DIFFRACTION97
1.3635-1.38150.19211760.18133135X-RAY DIFFRACTION97
1.3815-1.40040.21431620.17793173X-RAY DIFFRACTION97
1.4004-1.42040.1821610.17563157X-RAY DIFFRACTION97
1.4204-1.44160.18811800.16923150X-RAY DIFFRACTION97
1.4416-1.46410.18561560.16443234X-RAY DIFFRACTION98
1.4641-1.48810.19841610.15923138X-RAY DIFFRACTION97
1.4881-1.51380.17031640.15683197X-RAY DIFFRACTION98
1.5138-1.54130.17151710.16223195X-RAY DIFFRACTION98
1.5413-1.5710.1661570.15413183X-RAY DIFFRACTION98
1.571-1.6030.17551580.15683177X-RAY DIFFRACTION98
1.603-1.63790.16411600.15073214X-RAY DIFFRACTION99
1.6379-1.6760.16371880.15283206X-RAY DIFFRACTION99
1.676-1.71790.18221850.15063225X-RAY DIFFRACTION99
1.7179-1.76440.19111770.15253197X-RAY DIFFRACTION99
1.7644-1.81630.17071880.15853213X-RAY DIFFRACTION99
1.8163-1.87490.1661690.15443206X-RAY DIFFRACTION99
1.8749-1.94190.16871560.15393265X-RAY DIFFRACTION99
1.9419-2.01960.18961670.14643250X-RAY DIFFRACTION99
2.0196-2.11150.16931970.15393209X-RAY DIFFRACTION100
2.1115-2.22280.18731790.15123272X-RAY DIFFRACTION99
2.2228-2.36210.15761780.15183229X-RAY DIFFRACTION100
2.3621-2.54440.1661660.1573272X-RAY DIFFRACTION100
2.5444-2.80030.18961490.1633315X-RAY DIFFRACTION100
2.8003-3.20520.17911700.16273287X-RAY DIFFRACTION100
3.2052-4.0370.15031500.14363330X-RAY DIFFRACTION100
4.037-32.36790.15771860.16463257X-RAY DIFFRACTION97

+
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