[English] 日本語
Yorodumi
- PDB-1snf: MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1snf
TitleMYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND DEOXYURIDINE 5'-MONOPHOSPHATE
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / jelly-roll / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


dUTP metabolic process / 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
NITRATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. ...Sawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. / Rogers, Y.C. / Park, M.S. / Waldo, G.S. / Pashkov, I. / Cascio, D. / Yeates, T.O. / Perry, J.L. / Terwilliger, T.C. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.
Authors: Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. / Rogers, Y.C. / Park, M.S. / Waldo, G.S. / Pashkov, I. / Cascio, D. / Perry, J.L. / Sawaya, M.R.
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,40514
Polymers53,9773
Non-polymers1,42811
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-65 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.228, 77.496, 93.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homo-trimer. It is contained in the asymmetric unit.

-
Components

-
Protein , 1 types, 3 molecules ABC

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


Mass: 17992.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PRO
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase

-
Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N2O8P
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.52 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, magnesium nitrate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2002 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→80 Å / Num. all: 36211 / Num. obs: 36211 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3579 / Rsym value: 0.462 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MQ7

1mq7


Resolution: 1.85→41.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.216 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20462 3485 10 %RANDOM
Rwork0.16931 ---
all0.173 31243 --
obs0.17293 31243 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---1.88 Å20 Å2
3---2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 91 246 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213048
X-RAY DIFFRACTIONr_bond_other_d0.0020.022972
X-RAY DIFFRACTIONr_angle_refined_deg2.7162.0184163
X-RAY DIFFRACTIONr_angle_other_deg1.37336836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925393
X-RAY DIFFRACTIONr_chiral_restr0.1220.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023358
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02570
X-RAY DIFFRACTIONr_nbd_refined0.1850.2426
X-RAY DIFFRACTIONr_nbd_other0.2480.23458
X-RAY DIFFRACTIONr_nbtor_other0.0840.22007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2205
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3520.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.213
X-RAY DIFFRACTIONr_mcbond_it0.9891.51981
X-RAY DIFFRACTIONr_mcangle_it1.62123181
X-RAY DIFFRACTIONr_scbond_it2.6231067
X-RAY DIFFRACTIONr_scangle_it4.3874.5982
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 262
Rwork0.256 2051
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)
10.16370.01650.12210.61540.13610.6578-0.01250.0165-0.0229-0.0774-0.02970.01110.1581-0.01370.04220.0603-0.00340.01350.0138-0.00770.026113.126-9.1-8.802
20.6658-0.3442-0.21040.57680.12660.6004-0.0158-0.06360.0155-0.0010.06160.06070.0348-0.0601-0.04580.0048-0.01040.00420.0241-0.00290.02952.4672.3882.368
30.6-0.05840.34560.5206-0.10470.3802-0.0010.0066-0.00380.0558-0.0103-0.09390.04150.03050.01130.02040.01350.00430.02520.00170.025221.3890.3415.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 13024 - 150
2X-RAY DIFFRACTION2BB4 - 13024 - 150
3X-RAY DIFFRACTION3CC4 - 13024 - 150

+
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