[English] 日本語
Yorodumi
- PDB-5hwu: Crystal Structure of DR2231_E46A mutant in complex with dUMPNPP a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hwu
TitleCrystal Structure of DR2231_E46A mutant in complex with dUMPNPP and Manganese
ComponentsDR2231
KeywordsHYDROLASE / alpha helix
Function / homology
Function and homology information


nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function
putative ntp pyrophosphohydrolase like fold / putative ntp pyrophosphohydrolase like domain / NTP pyrophosphohydrolase-like domain superfamily / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / : / HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMota, C.S. / Goncalves, A.M.D. / de Sanctis, D.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e tecnologiaSFRH/BEST/51724/2011 Portugal
CitationJournal: FEBS J. / Year: 2016
Title: Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP.
Authors: Mota, C.S. / Goncalves, A.M. / de Sanctis, D.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Apr 4, 2018Group: Data collection / Structure summary / Category: audit_author / entity / struct
Item: _audit_author.name / _entity.pdbx_description / _struct.pdbx_descriptor
Revision 1.4Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / 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: DR2231
B: DR2231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6747
Polymers29,9502
Non-polymers7245
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-72 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.263, 78.014, 141.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-355-

HOH

-
Components

#1: Protein DR2231


Mass: 14974.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Gene: DR_2231 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9RS96
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.42 Å3/Da / Density % sol: 49.08 % / Mosaicity: 0.37 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: Lithium Acetate, PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.1→41.521 Å / Num. obs: 17331 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.85 Å2 / Rsym value: 0.104 / Net I/av σ(I): 7.13 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.213.50.6361.21100
2.21-2.353.50.4311.8199.9
2.35-2.513.50.3172.5199.8
2.51-2.713.50.2443.2199.9
2.71-2.973.50.1555.1199.9
2.97-3.323.50.0978.11100
3.32-3.833.40.05812.9199.6
3.83-4.73.30.04216.9199.6
4.7-6.643.30.04216.3199.3
6.64-41.5213.20.02522.4198.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2YFC

2yfc


Resolution: 2.1→41.521 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.247 1640 5.04 %
Rwork0.201 --
obs0.2033 17302 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.27 Å2 / Biso mean: 32.5731 Å2 / Biso min: 13.33 Å2
Refinement stepCycle: final / Resolution: 2.1→41.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 37 156 2243
Biso mean--24.13 38.82 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072146
X-RAY DIFFRACTIONf_angle_d0.8672901
X-RAY DIFFRACTIONf_chiral_restr0.039322
X-RAY DIFFRACTIONf_plane_restr0.007387
X-RAY DIFFRACTIONf_dihedral_angle_d19.103805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.16180.28421270.267425852712100
2.1618-2.23160.35611350.260626192754100
2.2316-2.31130.2991290.245825562685100
2.3113-2.40390.25771660.23082551271799
2.4039-2.51320.32011390.214125612700100
2.5132-2.64570.26871550.220425722727100
2.6457-2.81150.27451210.206225812702100
2.8115-3.02850.27381640.193825632727100
3.0285-3.33310.24361310.18912604273599
3.3331-3.81510.20471580.16772529268799
3.8151-4.80550.1715920.16882619271199
4.8055-41.52940.23831230.2062569269299
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)
10.1397-0.1244-0.0660.28290.12960.274-0.0384-0.5847-0.20970.1756-0.02720.24550.1224-0.1164-0.00050.27980.01750.03750.3812-0.00830.26870.901110.7315-8.6664
21.686-0.0581-0.57870.64470.09160.7187-0.0239-0.17330.10290.01210.0428-0.0235-0.0640.01320.06950.1977-0.01540.01480.1378-0.03680.200312.017917.8352-20.628
30.7559-0.98740.37931.76-0.36590.2743-0.09120.5421-0.2718-0.099-0.0894-0.39130.5038-0.346-0.21920.2865-0.03240.04010.2958-0.08480.245918.65965.8243-38.1634
41.1235-1.41090.91311.9821-1.12970.7668-0.50510.3136-0.88160.07930.32920.47810.0202-0.51850.36450.3567-0.12960.1260.2855-0.14060.4635-0.3976-1.2472-25.3652
50.3493-0.2445-0.46430.22470.23390.8746-0.1575-0.2326-0.10110.12860.1247-0.07640.22390.42140.03060.24640.01150.02070.2016-0.00410.2223.41476.3945-21.548
60.705-0.2677-0.1820.04370.19380.6066-0.08760.6365-0.024-0.02470.00050.0066-0.0713-0.2234-0.01120.20010.0069-0.00060.1881-0.00160.18946.576217.572-29.6128
70.6945-0.4619-0.47610.49460.00890.6849-0.0517-0.0845-0.00570.0283-0.00250.04670.0475-0.035-0.00140.1756-0.00890.00660.1996-0.04040.15348.865312.9093-17.9668
80.16720.0383-0.05370.15440.0520.53530.0736-0.7010.21060.0736-0.0311-0.0157-0.32070.62-0.73130.3815-0.0450.0190.625-0.19390.360419.587422.2202-4.1373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 33 )A7 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 112 )A34 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 127 )A113 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 144 )A128 - 144
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 33 )B7 - 33
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 63 )B34 - 63
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 112 )B64 - 112
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 144 )B113 - 144

+
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