[English] 日本語
Yorodumi
- PDB-3mz5: Crystal structure of Staphylococcal nuclease variant Delta+PHS L1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mz5
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L103A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / 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) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B. / Heroux, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Cavities determine the pressure unfolding of proteins.
Authors: Roche, J. / Caro, J.A. / Norberto, D.R. / Barthe, P. / Roumestand, C. / Schlessman, J.L. / Garcia, A.E. / Garcia-Moreno E, B. / Royer, C.A.
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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_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_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: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5443
Polymers16,1011
Non-polymers4422
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.068, 60.504, 38.032
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 16101.383 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: G50F,V51N,L103A,P117G,H124L,S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 18916 / Num. obs: 18916 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.044 / Χ2: 1.501 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.58-1.616.10.1938490.974190.2
1.61-1.646.30.1739270.984192.7
1.64-1.676.50.1688991.011196.5
1.67-1.76.90.1539400.952197.8
1.7-1.7470.1439570.971198.6
1.74-1.787.30.1249221.005198.7
1.78-1.827.30.1069931.081199.5
1.82-1.877.40.0979381.117199.3
1.87-1.937.40.0819541.227199.3
1.93-1.997.40.079581.283199.6
1.99-2.067.40.0639671.421199.5
2.06-2.147.40.0559481.465199.7
2.14-2.247.40.059781.57199.5
2.24-2.367.40.0499521.624199.8
2.36-2.517.40.0479681.865199.9
2.51-2.77.30.0499722.211100
2.7-2.977.20.0469812.4251100
2.97-3.47.10.0389722.422199.7
3.4-4.296.90.0339422.066196.6
4.29-506.70.0328992.067189.9

-
Phasing

Phasing MRRfactor: 36.59 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.66 Å
Translation2.5 Å23.66 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, T82A, L103A, Y113A, V114A, Y115A; all b-factors were reset to 20.

3bdc


Resolution: 1.58→30.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.832 / SU B: 1.823 / SU ML: 0.066 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1875 9.9 %RANDOM
Rwork0.19 ---
all0.238 19289 --
obs0.194 18883 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.13 Å2 / Biso mean: 23.439 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20.83 Å2
2---1.46 Å20 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 1.58→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 26 76 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221120
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.0061522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.222548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02515220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.587155
X-RAY DIFFRACTIONr_chiral_restr0.1270.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021817
X-RAY DIFFRACTIONr_mcbond_it1.5481.5663
X-RAY DIFFRACTIONr_mcangle_it2.32521072
X-RAY DIFFRACTIONr_scbond_it3.1893457
X-RAY DIFFRACTIONr_scangle_it4.6224.5442
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 134 -
Rwork0.243 1133 -
all-1267 -
obs--91.09 %

+
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