[English] 日本語
Yorodumi
- PDB-2hr6: Crystal structure of dUTPase in complex with substrate analogue d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hr6
TitleCrystal structure of dUTPase in complex with substrate analogue dUDP and manganese
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / JELLY ROLL / ENZYME-LIGAND-metal COMPLEX
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / protein homotrimerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
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'-DIPHOSPHATE / : / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsBarabas, O. / Kovari, J. / Tapai, R. / Vertessy, B.G.
Citation
Journal: Proteins / Year: 2008
Title: Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Authors: Kovari, J. / Barabas, O. / Varga, B. / Bekesi, A. / Tolgyesi, F. / Fidy, J. / Nagy, J. / Vertessy, B.G.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase.
Authors: Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Atomic Resolution Structure of Escherichia Coli Dutpase Determined Ab Initio
Authors: Gonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E.
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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 / _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)16,8084
Polymers16,3031
Non-polymers5053
Water2,810156
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)50,42312
Polymers48,9083
Non-polymers1,5169
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12690 Å2
ΔGint-89 kcal/mol
Surface area15910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.049, 75.049, 99.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1089-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y,1+x-y,z and -x+y,1-x,z

-
Components

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


Mass: 16302.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dut / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06968, dUTP diphosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2002 / Details: mirror
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.84→24.9 Å / Num. all: 14703 / Num. obs: 14703 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 22.35 Å2 / Rsym value: 0.064 / Net I/σ(I): 10.8
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 815 / Rsym value: 0.558 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUW
Resolution: 1.84→24.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.48 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17338 749 5.1 %RANDOM
Rwork0.15054 ---
all0.15168 13953 --
obs0.15168 13953 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.763 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.84→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 29 156 1198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221073
X-RAY DIFFRACTIONr_bond_other_d0.0020.021005
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.011465
X-RAY DIFFRACTIONr_angle_other_deg0.82132326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3224.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12115168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.193155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021180
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02196
X-RAY DIFFRACTIONr_nbd_refined0.2150.2122
X-RAY DIFFRACTIONr_nbd_other0.1910.2888
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2490
X-RAY DIFFRACTIONr_nbtor_other0.0820.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.217
X-RAY DIFFRACTIONr_mcbond_it2.232714
X-RAY DIFFRACTIONr_mcbond_other0.0932282
X-RAY DIFFRACTIONr_mcangle_it3.606101107
X-RAY DIFFRACTIONr_scbond_it6.0120410
X-RAY DIFFRACTIONr_scangle_it7.99350356
LS refinement shellResolution: 1.842→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 58 -
Rwork0.189 832 -
obs-890 82.64 %
Refinement TLS params.Method: refined / Origin x: 0.1866 Å / Origin y: 31.3803 Å / Origin z: 4.8255 Å
111213212223313233
T-0.0609 Å2-0.0048 Å20.0184 Å2--0.0529 Å2-0.0189 Å2---0.0563 Å2
L0.2476 °2-0.0981 °2-0.0217 °2-0.808 °2-0.0553 °2--0.1993 °2
S-0.0404 Å °0.0061 Å °-0.0466 Å °-0.0298 Å °-0.0114 Å °-0.0463 Å °0.0264 Å °0.01 Å °0.0518 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1371 - 137
2X-RAY DIFFRACTION1AC7771

+
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