[English] 日本語
Yorodumi
- PDB-1vpy: CRYSTAL STRUCTURE OF a DUF72 family protein (EF0366) FROM ENTEROC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vpy
TitleCRYSTAL STRUCTURE OF a DUF72 family protein (EF0366) FROM ENTEROCOCCUS FAECALIS V583 AT 2.52 A RESOLUTION
ComponentsPROTEIN (hypothetical protein EF0366)
KeywordsUNKNOWN FUNCTION / TIM ALPHA/BETA BARREL FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


Protein of unknown function UPF0759 / Protein of unknown function DUF72 / UPF0759 superfamily / Protein of unknown function DUF72 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / : / DUF72 domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (ef0366) from Enterococcus faecalis v583 at 2.52 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: PROTEIN (hypothetical protein EF0366)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3616
Polymers34,0991
Non-polymers2625
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.079, 114.079, 52.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein PROTEIN (hypothetical protein EF0366)


Mass: 34099.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: ef0366 / Production host: Escherichia coli (E. coli) / References: GenBank: 29375004, UniProt: Q838R9*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.44 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 10.0% PEG-3000, 0.2M Zn(OAc)2, 0.1M Acetate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979694, 0.979571, 1.019859
DetectorType: ADSC / Detector: CCD / Date: Aug 27, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796941
20.9795711
31.0198591
ReflectionResolution: 2.52→28.52 Å / Num. obs: 13332 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.06 Å2 / Rsym value: 0.18 / Net I/σ(I): 9.1
Reflection shellResolution: 2.52→2.66 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1939 / Rsym value: 0.01038 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALACCP4 4.2data scaling
SHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.52→28.52 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.892 / SU B: 21.487 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.265
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) ELECTRON DENSITY IN TWO REGIONS, RESIDUES 11-19 AND 202-209 IS AMBIGUOUS AND THE STRUCTURE WAS NOT MODELED IN THESE REGIONS. 3) THE ...Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) ELECTRON DENSITY IN TWO REGIONS, RESIDUES 11-19 AND 202-209 IS AMBIGUOUS AND THE STRUCTURE WAS NOT MODELED IN THESE REGIONS. 3) THE ELECTRON DENSITY FOR THE SIDECHAIN OF CYS 71 INDICATES AN UNIDENTIFIED COVALENT MODIFICATION. 4) THE CRYSTALLIZATION CONTAINS 0.2M ZINC ACETATE; THEREFORE, SEVERAL ZN IONS WERE MODELED INTO ELECTRON DENSITY WITHIN COORDINATION DISTANCE OF POTENTIAL SIDECHAIN LIGANDS (I.E. HISTIDINE AND GLUTAMIC ACID).
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 657 4.9 %RANDOM
Rwork0.22493 ---
obs0.22652 12658 99.89 %-
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: 38.918 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å2-1.01 Å20 Å2
2---2.01 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.52→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 8 37 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222061
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9332799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52424.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23515315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.097157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021594
X-RAY DIFFRACTIONr_nbd_refined0.1970.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.23
X-RAY DIFFRACTIONr_mcbond_it0.3831.51281
X-RAY DIFFRACTIONr_mcangle_it0.61422019
X-RAY DIFFRACTIONr_scbond_it1.2463899
X-RAY DIFFRACTIONr_scangle_it1.6534.5780
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21396
LS refinement shellResolution: 2.52→2.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 47 4.81 %
Rwork0.306 930 -
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)
114.1434-21.85185.98634.5063-7.42067.0195-1.427-1.25730.17473.54341.10180.8008-0.9678-0.42280.32520.0179-0.05890.01770.12760.0139-0.091323.853625.663338.6457
23.81120.034-0.29255.22990.07511.80390.12730.29210.1789-0.397-0.2142-0.5659-0.06640.05520.0869-0.07150.0304-0.0163-0.09810.1006-0.118329.757832.676524.3682
39.7998-3.9192.07197.8959-1.10672.010.165-0.3212-0.20920.0539-0.19330.64520.0778-0.06380.0283-0.0867-0.0383-0.0355-0.0906-0.0165-0.160814.881924.325731.863
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-3 - 109 - 22
2221 - 20133 - 213
33210 - 265222 - 277

+
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