[English] 日本語
Yorodumi
- PDB-4lfy: Crystal structure of a dihydroorotase from Burkholderia cenocepac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lfy
TitleCrystal structure of a dihydroorotase from Burkholderia cenocepacia J2315
ComponentsDihydroorotase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / carboxylated lysine
Function / homology
Function and homology information


dihydroorotase / pyrimidine nucleobase biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding
Similarity search - Function
Dihydroorotase homodimeric type / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Amidohydrolase family / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia cenocepacia (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a dihydroorotase from Burkholderia cenocepacia J2315
Authors: Lukacs, C.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydroorotase
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,27112
Polymers81,7252
Non-polymers54610
Water10,773598
1
A: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1366
Polymers40,8621
Non-polymers2735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1366
Polymers40,8621
Non-polymers2735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-211 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.480, 89.870, 153.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999183, 0.033103, 0.023193), (0.015425, 0.842671, -0.538208), (-0.03736, -0.53741, -0.842493)-4.86403, 3.50955, 11.35663

-
Components

#1: Protein Dihydroorotase / / DHOase


Mass: 40862.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (unknown) / Strain: J2315 / Gene: pyrC, BceJ2315_32910, BCAL3351 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EEU0, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1M Tris HCl, 18% PEG4000, 0.2M CaCl2, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 69475 / Num. obs: 69409 / % possible obs: 99.9 % / Redundancy: 6.16 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.33
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.17 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.85 / Num. unique all: 5049 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j79
Resolution: 1.8→46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.881 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18714 3510 5.1 %RANDOM
Rwork0.15745 ---
obs0.15895 65822 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2--0.14 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 16 598 5968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195559
X-RAY DIFFRACTIONr_bond_other_d0.0010.025214
X-RAY DIFFRACTIONr_angle_refined_deg1.641.977589
X-RAY DIFFRACTIONr_angle_other_deg0.864311968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8565712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73422.373236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7515814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6631548
X-RAY DIFFRACTIONr_chiral_restr0.1010.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021274
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_it1.2731.5112842
X-RAY DIFFRACTIONr_mcbond_other1.2721.5112841
X-RAY DIFFRACTIONr_mcangle_it1.9752.2563556
X-RAY DIFFRACTIONr_mcangle_other1.9752.2563557
X-RAY DIFFRACTIONr_scbond_it1.6251.642717
X-RAY DIFFRACTIONr_scbond_other1.6241.642717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5392.4094034
X-RAY DIFFRACTIONr_long_range_B_refined4.7613.016590
X-RAY DIFFRACTIONr_long_range_B_other4.6112.3986351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 245 -
Rwork0.194 4800 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.084-0.00710.03960.2879-0.04420.5144-0.0044-0.0036-0.0087-0.009-0.00950.01660.02470.0530.01390.00660.0009-0.00160.00920.00610.00936.15778.080323.9651
20.1950.06580.2280.09110.19030.75730.06640.02920.03030.0559-0.02710.00190.11820.0014-0.03930.0407-0.00810.00880.02570.00330.0181-11.2941-2.5189-12.8588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 364
2X-RAY DIFFRACTION2B10 - 364

+
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