[English] 日本語
Yorodumi
- PDB-6ajd: Crystal structure of a monometallic dihydropyrimidinase from Pseu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ajd
TitleCrystal structure of a monometallic dihydropyrimidinase from Pseudomonas aeruginosa PAO1 reveals no lysine carbamylation within the active site
ComponentsD-hydantoinase/dihydropyrimidinase
KeywordsHYDROLASE / dihydropyrimidinase
Function / homology
Function and homology information


dihydropyrimidinase / dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-hydantoinase/dihydropyrimidinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.223 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structures of monometallic dihydropyrimidinase and the human dihydroorotase domain K1556A mutant reveal no lysine carbamylation within the active site
Authors: Cheng, J.H. / Huang, Y.H. / Lin, J.J. / Huang, C.Y.
History
DepositionAug 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-hydantoinase/dihydropyrimidinase
B: D-hydantoinase/dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3344
Polymers106,2032
Non-polymers1312
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-84 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.375, 110.169, 112.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein D-hydantoinase/dihydropyrimidinase / DHPase


Mass: 53101.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dht, PA0441 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I676, dihydropyrimidinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.54 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25%PEG4000, 100mM Tris-HCl pH8.5, 200mM Calcium Chloride

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.223→30 Å / Num. obs: 54478 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 3.9
Reflection shellResolution: 2.223→2.31 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 5383 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5C

5e5c


Resolution: 2.223→29.277 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2323 2760 5.07 %
Rwork0.1819 --
obs0.1844 54416 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.223→29.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 2 283 7627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087526
X-RAY DIFFRACTIONf_angle_d0.9810236
X-RAY DIFFRACTIONf_dihedral_angle_d7.8064424
X-RAY DIFFRACTIONf_chiral_restr0.0561112
X-RAY DIFFRACTIONf_plane_restr0.0061354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2234-2.26170.28291190.21412362X-RAY DIFFRACTION92
2.2617-2.30280.28111450.21752548X-RAY DIFFRACTION100
2.3028-2.34710.31081250.19952603X-RAY DIFFRACTION100
2.3471-2.3950.2631400.20542561X-RAY DIFFRACTION100
2.395-2.44710.30191340.21782549X-RAY DIFFRACTION100
2.4471-2.5040.28161350.20742579X-RAY DIFFRACTION100
2.504-2.56650.27011540.2052532X-RAY DIFFRACTION100
2.5665-2.63590.28081440.19892553X-RAY DIFFRACTION100
2.6359-2.71340.24341190.20482597X-RAY DIFFRACTION100
2.7134-2.80090.23911560.20112538X-RAY DIFFRACTION100
2.8009-2.90090.30241200.21142628X-RAY DIFFRACTION100
2.9009-3.0170.26971400.21472566X-RAY DIFFRACTION100
3.017-3.15410.24961510.20912596X-RAY DIFFRACTION100
3.1541-3.32020.26991480.20652562X-RAY DIFFRACTION100
3.3202-3.52790.24961400.20062617X-RAY DIFFRACTION100
3.5279-3.79980.18941330.16642590X-RAY DIFFRACTION100
3.7998-4.18120.21191280.15562635X-RAY DIFFRACTION100
4.1812-4.78390.17241350.13142626X-RAY DIFFRACTION99
4.7839-6.01860.20541300.15282679X-RAY DIFFRACTION100
6.0186-29.27920.1681640.15512735X-RAY DIFFRACTION98

+
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