[English] 日本語
Yorodumi
- PDB-3mpr: Crystal Structure of endonuclease/exonuclease/phosphatase family ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mpr
TitleCrystal Structure of endonuclease/exonuclease/phosphatase family protein from Bacteroides thetaiotaomicron, Northeast Structural Genomics Consortium Target BtR318A
ComponentsPutative endonuclease/exonuclease/phosphatase family protein
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


3'-5'-RNA exonuclease activity / endonuclease activity / metal ion binding
Similarity search - Function
: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / BROMIDE ION / DI(HYDROXYETHYL)ETHER / Unknown ligand / Endonuclease/exonuclease/phosphatase family protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.899 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target BtR318A
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / ...Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Putative endonuclease/exonuclease/phosphatase family protein
B: Putative endonuclease/exonuclease/phosphatase family protein
C: Putative endonuclease/exonuclease/phosphatase family protein
D: Putative endonuclease/exonuclease/phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,08334
Polymers138,3924
Non-polymers1,69130
Water22,0141222
1
A: Putative endonuclease/exonuclease/phosphatase family protein
B: Putative endonuclease/exonuclease/phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,01521
Polymers69,1962
Non-polymers81919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative endonuclease/exonuclease/phosphatase family protein
D: Putative endonuclease/exonuclease/phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06813
Polymers69,1962
Non-polymers87211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.643, 103.143, 79.811
Angle α, β, γ (deg.)90.00, 103.39, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative endonuclease/exonuclease/phosphatase family protein


Mass: 34597.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_3783 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8A183

-
Non-polymers , 5 types, 1252 molecules

#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 8 / Source method: obtained synthetically
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1222 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:LiBr 0.1M, NaAcetate 0.1M, PEG8000 20% v/v, microbatch under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97909 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 94601 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 16.18 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.899→39.474 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 4742 5.01 %
Rwork0.156 --
obs0.1584 94569 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.29 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1738 Å20 Å2-0.3088 Å2
2--4.6256 Å20 Å2
3----1.4518 Å2
Refinement stepCycle: LAST / Resolution: 1.899→39.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9021 0 60 1222 10303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069403
X-RAY DIFFRACTIONf_angle_d1.05512708
X-RAY DIFFRACTIONf_dihedral_angle_d13.4773413
X-RAY DIFFRACTIONf_chiral_restr0.0841281
X-RAY DIFFRACTIONf_plane_restr0.0051672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8992-1.92070.27181500.23432836X-RAY DIFFRACTION95
1.9207-1.94330.24941590.20232995X-RAY DIFFRACTION99
1.9433-1.9670.24421380.17912955X-RAY DIFFRACTION99
1.967-1.99190.22091520.16792956X-RAY DIFFRACTION99
1.9919-2.01810.22961480.16363015X-RAY DIFFRACTION99
2.0181-2.04580.2371510.16522996X-RAY DIFFRACTION99
2.0458-2.0750.21981810.17472946X-RAY DIFFRACTION99
2.075-2.1060.21431590.16472978X-RAY DIFFRACTION99
2.106-2.13890.25191310.15422998X-RAY DIFFRACTION100
2.1389-2.1740.221700.15412980X-RAY DIFFRACTION100
2.174-2.21140.22511610.15113011X-RAY DIFFRACTION100
2.2114-2.25160.20891590.16972975X-RAY DIFFRACTION99
2.2516-2.29490.21981510.16762953X-RAY DIFFRACTION99
2.2949-2.34180.21211510.15142986X-RAY DIFFRACTION100
2.3418-2.39270.20891660.14563006X-RAY DIFFRACTION100
2.3927-2.44840.181520.14772988X-RAY DIFFRACTION100
2.4484-2.50960.22851560.15343009X-RAY DIFFRACTION100
2.5096-2.57740.21141420.15453026X-RAY DIFFRACTION100
2.5774-2.65320.20321630.14972988X-RAY DIFFRACTION100
2.6532-2.73890.20061730.15182993X-RAY DIFFRACTION100
2.7389-2.83670.21411570.15333027X-RAY DIFFRACTION100
2.8367-2.95030.20661480.15063029X-RAY DIFFRACTION100
2.9503-3.08450.19561570.14922996X-RAY DIFFRACTION100
3.0845-3.2470.17991790.14212974X-RAY DIFFRACTION100
3.247-3.45040.17871570.14773040X-RAY DIFFRACTION100
3.4504-3.71660.17541520.13763025X-RAY DIFFRACTION100
3.7166-4.09020.16691560.13283018X-RAY DIFFRACTION100
4.0902-4.68130.1731790.12373029X-RAY DIFFRACTION100
4.6813-5.89480.16881720.1393026X-RAY DIFFRACTION100
5.8948-39.48260.21631720.19153073X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 48.0088 Å / Origin y: 43.2709 Å / Origin z: 24.1992 Å
111213212223313233
T0.001 Å2-0.0051 Å20.0031 Å2-0.007 Å20.0022 Å2--0.0049 Å2
L0.0645 °20.0261 °20.0261 °2-0.0828 °2-0.0275 °2--0.0919 °2
S0.001 Å °-0.0205 Å °0.0006 Å °0 Å °0.0053 Å °0.0055 Å °0.0176 Å °-0.0252 Å °-0.0065 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1311
2X-RAY DIFFRACTION1allB2 - 1232
3X-RAY DIFFRACTION1allC1 - 1310
4X-RAY DIFFRACTION1allD3 - 1311
5X-RAY DIFFRACTION1all1 - 33
6X-RAY DIFFRACTION1allU1 - 8
7X-RAY DIFFRACTION1allF1 - 15

+
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