[English] 日本語
Yorodumi
- PDB-2yfc: STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yfc
TitleSTRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH Mn and dUMP
ComponentsMAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
KeywordsHYDROLASE / DIMERIC DUTPASE
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'-MONOPHOSPHATE / HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGoncalves, A.M.D. / De Sanctis, D. / Mcsweeney, S.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans.
Authors: Goncalves, A.M.D. / Desanctis, D. / Mcsweeney, S.M.
History
DepositionApr 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references / Non-polymer description / Version format compliance
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_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.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_conn.ptnr2_label_seq_id / _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: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,14916
Polymers66,8354
Non-polymers1,31412
Water5,657314
1
A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0758
Polymers33,4172
Non-polymers6576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-70.6 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0758
Polymers33,4172
Non-polymers6576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-71.5 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.733, 150.191, 52.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99739, 0.07189, 0.00614), (0.07192, -0.9974, -0.00492), (0.00577, 0.00534, -0.99997)
Vector: 2.4283, -68.58492, 26.72167)

-
Components

#1: Protein
MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / DR2231


Mass: 16708.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RS96, nucleoside-triphosphate diphosphatase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.28 Å3/Da / Density % sol: 49.95 % / Description: NONE
Crystal growDetails: 0.18 M LITHIUM ACETATE AND 20% (W/V) PEG 3350, 10MM DUTP AND 10 MM MANGANESE CHLORIDE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 48355 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YF9

2yf9


Resolution: 2.01→20.001 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 2082 5 %
Rwork0.1775 --
obs0.1796 41628 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.377 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 24.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.6835 Å20 Å20 Å2
2---0.3526 Å20 Å2
3----0.1906 Å2
Refinement stepCycle: LAST / Resolution: 2.01→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 70 314 4480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124263
X-RAY DIFFRACTIONf_angle_d1.1515804
X-RAY DIFFRACTIONf_dihedral_angle_d15.0791623
X-RAY DIFFRACTIONf_chiral_restr0.069639
X-RAY DIFFRACTIONf_plane_restr0.005780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.05670.25321360.18792574X-RAY DIFFRACTION98
2.0567-2.10810.21551360.16672607X-RAY DIFFRACTION99
2.1081-2.1650.20841370.15882585X-RAY DIFFRACTION99
2.165-2.22870.2361370.15952602X-RAY DIFFRACTION99
2.2287-2.30050.21471380.16132635X-RAY DIFFRACTION99
2.3005-2.38260.21481400.1642654X-RAY DIFFRACTION99
2.3826-2.47780.24341380.17282605X-RAY DIFFRACTION99
2.4778-2.59040.26351370.18562615X-RAY DIFFRACTION99
2.5904-2.72660.27181400.18972657X-RAY DIFFRACTION100
2.7266-2.8970.2461400.19142658X-RAY DIFFRACTION100
2.897-3.11990.21271400.1942679X-RAY DIFFRACTION100
3.1199-3.43240.22861410.18352664X-RAY DIFFRACTION100
3.4324-3.92590.1791420.17162709X-RAY DIFFRACTION100
3.9259-4.93390.20371420.15862671X-RAY DIFFRACTION98
4.9339-20.00180.19641380.19892631X-RAY DIFFRACTION92
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)
10.5008-0.1851-0.10040.7198-0.42330.3446-0.1732-0.1542-0.0414-0.04980.00820.00040.13440.09830.10360.17860.03220.01320.15520.02010.1532-22.6612-58.895613.2917
20.16560.1320.06140.4299-0.5590.8289-0.0638-0.0279-0.03190.0760.0481-0.04-0.0067-0.02710.01120.0720.03360.00860.12170.01710.1057-24.3326-47.35630.1675
30.3885-0.328-0.15270.52550.4120.68360.07160.1831-0.2153-0.2078-0.00070.23930.0146-0.1084-0.04390.1229-0.0378-0.01340.1410.02720.1318-31.9262-50.3673-9.5722
40.04130.0157-0.10230.5338-0.15910.5506-0.0572-0.0309-0.0286-0.0104-0.0122-0.07710.13940.00720.01090.09590.02910.01140.08190.0120.086-20.1297-53.05771.3258
50.20840.23520.02550.3223-0.01130.5723-0.11180.06810.1859-0.16810.0155-0.0783-0.48130.0910.04320.26590.0155-0.00690.10990.03870.1673-24.3554-11.45912.9564
60.1345-0.1371-0.05480.7831-0.40710.9449-0.0089-0.03620.0076-0.0240.0085-0.0161-0.0962-0.0602-0.00470.06450.0063-0.01030.07820.01090.0739-24.9976-23.121926.4354
70.19980.1004-0.19510.81890.150.3096-0.0321-0.14990.14350.20170.07270.2698-0.0451-0.18960.01990.12990.06710.02960.13590.00430.1216-32.9728-20.750835.8615
80.1453-0.02430.18440.7498-0.28550.444-0.05890.0190.03760.0708-0.0041-0.0908-0.23290.07750.04560.115-0.0109-0.01060.0620.00830.1009-21.2774-17.19625.2073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:45)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46:144)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 7:28)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 29:145)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 7:45)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 46:143)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 7:28)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 29:144)

+
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