[English] 日本語
Yorodumi
- PDB-2pau: Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pau
TitleCrystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and dAMP
Components5'-deoxynucleotidase YfbR
KeywordsHYDROLASE / Nucleotidase / 5'-deoxynucleotidase / YfbR / HD domain phosphohydrolase
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide salvage / thymidylate 5'-phosphatase activity / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / dUMP biosynthetic process / cobalt ion binding / nucleotide binding / identical protein binding / cytoplasm
Similarity search - Function
5'-deoxynucleotidase YfbR / 5'-deoxynucleotidase YfbR-like / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain ...5'-deoxynucleotidase YfbR / 5'-deoxynucleotidase YfbR-like / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / 5'-deoxynucleotidase YfbR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZimmerman, M.D. / Proudfoot, M. / Yakunin, A. / Minor, W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
Authors: Zimmerman, M.D. / Proudfoot, M. / Yakunin, A. / Minor, W.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6357
Polymers45,7482
Non-polymers8865
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-52 kcal/mol
Surface area15010 Å2
MethodPISA
2
A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules

A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules

A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,90521
Polymers137,2456
Non-polymers2,65915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)135.595, 135.595, 54.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: D5M / End label comp-ID: D5M / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
14SERSERAA - D4 - 3016
22LYSLYSBB - G2 - 3014

-
Components

#1: Protein 5'-deoxynucleotidase YfbR / Nucleoside 5'-monophosphate phosphohydrolase / 5'-deoxyribonucleotidase


Mass: 22874.219 Da / Num. of mol.: 2 / Mutation: E72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfbR, b2291, JW2288 / Plasmid: Modified pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: P76491, 5'-nucleotidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6P
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M NH4 Citrate, 0.1 % w/v NDSB 256, 5 % w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2006
Details: LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution Si(111) double-crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25437 / Num. obs: 25437 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2 / Rsym value: 0.563 / % possible all: 82.7

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
REFMAC5.2.0005refinement
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WPH

1wph
PDB Unreleased entry


Resolution: 2.1→40.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.201 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.259 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COOT program has also been used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1028 5.1 %RANDOM
Rwork0.193 ---
all0.196 19971 --
obs0.196 19971 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 53 53 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212825
X-RAY DIFFRACTIONr_bond_other_d0.0020.022577
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.983830
X-RAY DIFFRACTIONr_angle_other_deg0.90235943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10824.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35115464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8211519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined0.2380.2690
X-RAY DIFFRACTIONr_nbd_other0.1830.22573
X-RAY DIFFRACTIONr_nbtor_refined0.190.21373
X-RAY DIFFRACTIONr_nbtor_other0.0930.21686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9831.51819
X-RAY DIFFRACTIONr_mcbond_other0.2761.5706
X-RAY DIFFRACTIONr_mcangle_it1.4522805
X-RAY DIFFRACTIONr_scbond_it2.41131147
X-RAY DIFFRACTIONr_scangle_it3.6154.51025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2618 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.510.5
medium thermal0.792
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 72 -
Rwork0.25 1270 -
obs--82.74 %

+
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