[English] 日本語
Yorodumi
- PDB-2pfs: Crystal structure of universal stress protein from Nitrosomonas e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pfs
TitleCrystal structure of universal stress protein from Nitrosomonas europaea
ComponentsUniversal stress protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / stress protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


nucleotide binding / cytoplasm
Similarity search - Function
Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Universal stress protein
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsChruszcz, M. / Evdokimova, E. / Cymborowski, M. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Evol Appl / Year: 2013
Title: Structural and functional insight into the universal stress protein family.
Authors: Tkaczuk, K.L. / Shumilin, I.A. / Chruszcz, M. / Evdokimova, E. / Savchenko, A. / Minor, W.
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 14, 2011Group: Derived calculations
Revision 1.4Apr 17, 2013Group: Database references
Revision 1.5Jun 26, 2013Group: Database references
Revision 1.6Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Universal stress protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8273
Polymers16,7571
Non-polymers712
Water72140
1
A: Universal stress protein
hetero molecules

A: Universal stress protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6556
Polymers33,5132
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2140 Å2
ΔGint-52 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 76.000, 42.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein Universal stress protein / / Usp


Mass: 16756.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE1028 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q82VN8
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% PEG3350, 2% Isopropanol, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 6882 / Num. obs: 6882 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 58.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / Num. unique all: 277 / Rsym value: 0.486 / % possible all: 81.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
CCP4phasing
MLPHAREphasing
DMphasing
Omodel building
Cootmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.231 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.277 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25455 329 4.8 %RANDOM
Rwork0.19471 ---
all0.19758 6538 --
obs0.19758 6538 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0.9 Å20 Å2
2---1.8 Å20 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 2 40 978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021957
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9531308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4635124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8825.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.282154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1821.5647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7421006
X-RAY DIFFRACTIONr_scbond_it2.7363352
X-RAY DIFFRACTIONr_scangle_it4.2524.5302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 20 -
Rwork0.199 407 -
obs--83.07 %
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)
111.9458-4.86953.52443.9491-0.77591.26210.0194-0.8252-1.0076-0.11270.13680.31620.1841-0.1601-0.1563-0.1725-0.00890.0133-0.12420.0155-0.08165.885728.997117.1948
210.051-3.27180.22665.7113-1.43972.5845-0.1434-0.21080.3651-0.04890.1067-0.12070.02290.00510.0367-0.16450.04420.023-0.1822-0.0286-0.177711.860334.707518.2779
310.06613.06397.55950.93262.30095.6771.1132-0.7862-0.55340.2488-0.1528-0.16190.7903-0.8214-0.96040.1747-0.0976-0.21990.3257-0.11740.342-13.679823.18515.071
46.8401-1.13593.09850.1887-0.51962.78480.37210.2271-1.3816-0.43960.08750.2890.5125-0.0443-0.45960.0376-0.0013-0.0362-0.0799-0.0870.13851.317625.961310.4891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 204 - 22
2X-RAY DIFFRACTION2AA21 - 3523 - 37
3X-RAY DIFFRACTION3AA36 - 6038 - 62
4X-RAY DIFFRACTION4AA61 - 14563 - 147

+
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