[English] 日本語
Yorodumi
- PDB-3t16: Crystal structure of Staphylococcal nuclease variant NVIAGA/M98G ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t16
TitleCrystal structure of Staphylococcal nuclease variant NVIAGA/M98G at cryogenic temperature
ComponentsThermonucleaseMicrococcal nuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant
Function / homology
Function and homology information


endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSchlessman, J.L. / Doctrow, B.M. / Garcia-Moreno E., B. / Heroux, A.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant NVIAGA/M98G at cryogenic temperature
Authors: Baran, K.L. / Doctrow, B.M. / Chimenti, M. / Herbst, K. / Fitch, C.A. / Majumdar, A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJul 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thermonuclease


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.649, 48.649, 63.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Thermonuclease / Micrococcal nuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 16706.219 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: D21N/T33V/T41I/S59A/M98G/P117G/S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 41% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 13663 / Num. obs: 13663 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.681 / Net I/σ(I): 22
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8314.80.2956681.0341100
1.83-1.8614.90.2377101.0261100
1.86-1.9150.2326751.0771100
1.9-1.9414.90.1696881.1771100
1.94-1.98150.136491.2681100
1.98-2.03150.1227181.3381100
2.03-2.08150.0996681.41100
2.08-2.1314.90.0816881.5311100
2.13-2.2150.0756681.6011100
2.2-2.2714.90.0656861.5521100
2.27-2.35150.066901.5921100
2.35-2.4414.90.0556921.6771100
2.44-2.5514.90.056721.6951100
2.55-2.69150.0456891.8061100
2.69-2.8614.90.0446941.8451100
2.86-3.0814.80.0456842.3991100
3.08-3.3914.60.0446782.883199.9
3.39-3.8814.20.0436962.9951100
3.88-4.8813.50.0327022.046199.7
4.88-5013.50.0316481.804191.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.53 Å
Translation2.5 Å26.53 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RDF

2rdf


Resolution: 1.8→48.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2256 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8226 / SU B: 6.933 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1171 / SU Rfree: 0.1114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 678 5 %RANDOM
Rwork0.1811 ---
all0.1825 13637 --
obs0.1825 13637 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.83 Å2 / Biso mean: 44.2723 Å2 / Biso min: 26.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 71 1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221025
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9721379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45224.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90615200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.942155
X-RAY DIFFRACTIONr_chiral_restr0.1380.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021754
X-RAY DIFFRACTIONr_mcbond_it1.1671.5621
X-RAY DIFFRACTIONr_mcangle_it1.9532993
X-RAY DIFFRACTIONr_scbond_it3.6833404
X-RAY DIFFRACTIONr_scangle_it5.9434.5383
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 53 -
Rwork0.243 958 -
all-1011 -
obs--100 %
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)
19.41585.94544.08123.487-1.340314.15980.2119-0.2560.7515-0.17360.44721.47370.3032-2.0763-0.65910.47960.0255-0.06480.61010.13590.4368-12.4316.265-4.76
25.48512.21810.67562.87671.33747.45150.30910.1842-0.4296-0.11690.1562-0.00591.2620.0304-0.46530.630.0718-0.10180.30010.0180.2073-0.8998.536-3.904
30.98550.62782.80133.4833.076915.3379-0.08480.29850.21590.03720.4888-0.6194-0.4082.0202-0.4040.49130.00060.01360.6199-0.08850.30948.24221.3040.036
48.21023.9888-0.56265.74810.20510.62050.2769-0.4921-0.33160.44060.1575-0.40351.05690.505-0.43440.55210.123-0.06270.41620.02320.21143.88413.4238.423
51.67371.2962.0024.1367-2.20068.80870.0623-0.043-0.0062-0.0890.09760.1670.0619-0.5718-0.15990.46870.0305-0.01580.35210.03680.1904-5.49717.08-6.753
61.78661.70141.09742.67510.359.66270.01180.0455-0.0488-0.02030.06020.02440.099-0.0571-0.0720.44740.04980.00210.32810.04390.1675-1.94416.717-4.287
71.85490.4132.14592.13862.26599.371-0.07880.12210.0489-0.37290.2040.05-1.03240.4248-0.12520.54190.00590.03460.3444-0.00590.16741.31525.684-1.111
87.29350.07186.06122.57222.659617.6226-0.17760.07340.4042-0.79490.0945-0.1476-2.53510.29090.08320.9294-0.01850.06710.2754-0.00970.1521.48233.2643.68
910.4562-0.1674-0.075612.153-2.170717.08880.05250.04170.1429-0.56410.614-0.9599-1.16492.0523-0.66650.536-0.24010.09780.7296-0.19090.23610.4330.11610.719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 12
2X-RAY DIFFRACTION2A13 - 34
3X-RAY DIFFRACTION3A35 - 55
4X-RAY DIFFRACTION4A56 - 68
5X-RAY DIFFRACTION5A69 - 84
6X-RAY DIFFRACTION6A85 - 96
7X-RAY DIFFRACTION7A97 - 121
8X-RAY DIFFRACTION8A122 - 134
9X-RAY DIFFRACTION9A135 - 141

+
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