[English] 日本語
Yorodumi
- PDB-1ztv: Crystal structure of a duf72 family protein (ef0366) from enteroc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ztv
TitleCrystal structure of a duf72 family protein (ef0366) from enterococcus faecalis v583 at 3.10 A resolution
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / Tim alpha/beta barrel fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyProtein of unknown function UPF0759 / Protein of unknown function DUF72 / UPF0759 superfamily / Protein of unknown function DUF72 / TIM Barrel / Alpha-Beta Barrel / metal ion binding / Alpha Beta / DUF72 domain-containing protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (29342463) from Enterococcus faecalis V583 at 3.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3314
Polymers67,2612
Non-polymers712
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.819, 92.358, 119.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 274 / Label seq-ID: 13 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein hypothetical protein


Mass: 33630.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: 29342463 / Production host: Escherichia coli (E. coli) / References: UniProt: Q838R9
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.08 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 1.0M NaCitrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979224
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2004
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979224 Å / Relative weight: 1
ReflectionResolution: 3.1→119.52 Å / Num. obs: 18876 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
3.1-3.2799.73.50.3921.927200.392
3.27-3.4799.63.40.2453.125510.245
3.47-3.7199.43.40.1564.724190.156
3.71-499.73.40.1096.722710.109
4-4.3899.83.40.0779.420990.077
4.38-4.999.63.40.0541318940.054
4.9-5.6699.53.30.0513.716960.05
5.66-6.9398.63.20.0531214280.053
6.93-9.897.73.10.03715.611210.037
9.8-119.5298.83.10.01925.16770.019

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: molecular replacement
Starting model: pdb entry 1vpy

1vpy


Resolution: 3.1→73.13 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 27.071 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 3.517 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 975 5.2 %RANDOM
Rwork0.191 ---
all0.193 ---
obs0.19257 17862 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 77.153 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---1.31 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→73.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 2 12 4433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224542
X-RAY DIFFRACTIONr_bond_other_d0.0020.023939
X-RAY DIFFRACTIONr_angle_refined_deg0.6471.9366189
X-RAY DIFFRACTIONr_angle_other_deg0.53939134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.425552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67424.693228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28915703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.971518
X-RAY DIFFRACTIONr_chiral_restr0.0590.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025128
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02954
X-RAY DIFFRACTIONr_nbd_refined0.2010.31037
X-RAY DIFFRACTIONr_nbd_other0.1710.34205
X-RAY DIFFRACTIONr_nbtor_refined0.1880.52277
X-RAY DIFFRACTIONr_nbtor_other0.0840.52411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5173
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.060.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1250.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.51
X-RAY DIFFRACTIONr_mcbond_it0.80932837
X-RAY DIFFRACTIONr_mcbond_other0.14731108
X-RAY DIFFRACTIONr_mcangle_it1.37654461
X-RAY DIFFRACTIONr_scbond_it2.26881976
X-RAY DIFFRACTIONr_scangle_it3.46111728
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4094 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.330.5
MEDIUM THERMAL0.292
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 89 -
Rwork0.312 1284 -
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)
12.54780.196-0.28712.2581-0.93861.86230.059-0.446-0.53970.0979-0.3575-0.2372-0.01430.20780.2985-0.24830.0111-0.0962-0.02280.156-0.268919.1-23.483-2.086
22.4218-0.05920.16722.75880.06952.1684-0.06470.13950.2434-0.4757-0.05650.3392-0.1730.04450.1212-0.03410.0865-0.1341-0.22540.0273-0.42950.826-5.497-27.813
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-3 - 2759 - 287
22BB1 - 27013 - 282

+
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://pdbjlvh1.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