[English] 日本語
Yorodumi
- PDB-3mdx: Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mdx
TitleCrystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, rhombohedral crystal form
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / DEOXYURIDINE 5-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / Metal-binding / Nucleotide metabolism / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, rhombohedral crystal form
Authors: Abendroth, J. / Gardberg, A.S. / Staker, B.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0312
Polymers18,9691
Non-polymers621
Water3,261181
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0926
Polymers56,9063
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11960 Å2
ΔGint-39 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.880, 67.880, 95.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

-
Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 18968.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 2308 / Gene: dut, BAB1_1687 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YRG4, dUTP diphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: MD PACT SCREEN, E12: 20% PEG 3350, 200MM NA MALONATE, BRABA.10050.A AT 9.7MG/ML, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50.12 Å / Num. all: 29210 / Num. obs: 29143 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 30.1
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2204 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3MBQ, orthorhombic crystal form

3mbq


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.879 / SU ML: 0.033 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1475 5.1 %RANDOM
Rwork0.15 ---
all0.151 29210 --
obs0.151 29143 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 4 181 1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221097
X-RAY DIFFRACTIONr_bond_other_d0.0010.02765
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9961496
X-RAY DIFFRACTIONr_angle_other_deg0.97831864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3785150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.93422.91748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.05315182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1041513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
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_it1.0911.5707
X-RAY DIFFRACTIONr_mcbond_other0.3251.5291
X-RAY DIFFRACTIONr_mcangle_it1.85621137
X-RAY DIFFRACTIONr_scbond_it2.6643390
X-RAY DIFFRACTIONr_scangle_it4.2334.5352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 122 -
Rwork0.231 2073 -
obs--99.95 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5275-0.3829-0.53981.46410.19720.83750.0882-0.06460.04840.17250.06840.25-0.1332-0.1791-0.15660.07580.04610.09580.09140.02650.121119.542-5.7683.308
20.4785-0.92511.16922.6503-0.59921.97520.0285-0.04580.0108-0.17290.1650.1953-0.1408-0.2396-0.19350.03740.01640.02660.08870.0870.120221.333-6.834-15.478
30.4174-0.115-0.10330.8370.35160.79980.0679-0.05140.08340.00360.06550.0453-0.0385-0.0635-0.13340.05060.00950.03270.06010.00830.075129.108-9.969-4.792
42.8182-1.5805-0.74580.10310.64113.5030.1589-0.12030.0121-0.08350.04640.0810.1646-0.5716-0.20530.0588-0.0120.01810.11660.09370.126418.815-11.085-14.465
50.8943-0.20550.40960.593-0.16480.8279-0.0168-0.1650.00240.1760.0963-0.0989-0.02680.0022-0.07950.0578-0.0022-0.03140.0708-0.03930.054646.27-18.4726.866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 34
2X-RAY DIFFRACTION2A35 - 53
3X-RAY DIFFRACTION3A54 - 110
4X-RAY DIFFRACTION4A111 - 124
5X-RAY DIFFRACTION5A125 - 151

+
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