[English] 日本語
Yorodumi
- PDB-2b06: Crystal structure of the MutT/nudix family protein from Streptoco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b06
TitleCrystal structure of the MutT/nudix family protein from Streptococcus pneumoniae
ComponentsMutT/nudix family protein
KeywordsStructural Genomics/Unknown Function / MutT/nudix / Streptococcus pneumoniae / Structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Structural Genomics-Unknown Function COMPLEX
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / MutT/nudix family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsZhang, R. / Zhou, M. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.4 A crystal structure of the MutT/nudix family protein from Streptococcus pneumoniae
Authors: Zhang, R. / Zhou, M. / Abdullah, J. / Collart, F. / Joachimiak, A.
History
DepositionSep 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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_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.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_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_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: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0372
Polymers18,0121
Non-polymers241
Water4,089227
1
A: MutT/nudix family protein
hetero molecules

A: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0734
Polymers36,0242
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)65.850, 64.990, 41.779
Angle α, β, γ (deg.)90.00, 127.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-358-

HOH

31A-398-

HOH

DetailsThis protein existed as dimer. The second molecule of the dimer is generated by the two fold axis: -x, y,-z

-
Components

#1: Protein MutT/nudix family protein


Mass: 18012.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 14972717, UniProt: A0A0H2UQ81*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.94 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris/HCl, 0.2M MgSO4, 25% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 25116 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5382 / % possible all: 79.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→40.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.151 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21923 1318 5 %RANDOM
Rwork0.1889 ---
all0.19046 26059 --
obs0.19046 25116 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å2-1.01 Å2
2--1.29 Å20 Å2
3----1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.035 Å0.028 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.4→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 1 227 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221268
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9591722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44225.15266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6615222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.294157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02987
X-RAY DIFFRACTIONr_nbd_refined0.1980.2531
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2182
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.250
X-RAY DIFFRACTIONr_mcbond_it0.7861.5784
X-RAY DIFFRACTIONr_mcangle_it1.24521234
X-RAY DIFFRACTIONr_scbond_it1.9273565
X-RAY DIFFRACTIONr_scangle_it2.774.5488
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 71 -
Rwork0.233 1597 -
obs--83.53 %
Refinement TLS params.Method: refined / Origin x: 5.6868 Å / Origin y: 49.4099 Å / Origin z: 11.1713 Å
111213212223313233
T-0.0316 Å20.0056 Å2-0.0066 Å2--0.0123 Å20.0043 Å2---0.0395 Å2
L1.0636 °20.1375 °2-0.1155 °2-0.3917 °20.1723 °2--1.1355 °2
S0.007 Å °-0.1269 Å °0.0198 Å °-0.0036 Å °-0.0187 Å °-0.0236 Å °0.0418 Å °0.0989 Å °0.0117 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 281 - 28
2X-RAY DIFFRACTION1AA35 - 10035 - 100
3X-RAY DIFFRACTION1AA101 - 155101 - 155

+
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