[English] 日本語
Yorodumi
- PDB-3cex: Crystal structure of the conserved protein of locus EF_3021 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cex
TitleCrystal structure of the conserved protein of locus EF_3021 from Enterococcus faecalis
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / EF_3021 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Mycothiol-S-transferase / DinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / DinB-like domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the conserved protein of locus EF_3021 from Enterococcus faecalis.
Authors: Cuff, M.E. / Wu, R. / Moy, S. / Joachimiak, A.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8816
Polymers39,5772
Non-polymers3044
Water3,387188
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8816
Polymers39,5772
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3350 Å2
ΔGint-17.1 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8816
Polymers39,5772
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3370 Å2
ΔGint-18.3 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.191, 55.137, 62.429
Angle α, β, γ (deg.)90.000, 108.200, 90.000
Int Tables number3
Space group name H-MP121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

-
Components

#1: Protein Uncharacterized protein


Mass: 19788.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_3021 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZN0
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M Trisodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→35.9 Å / Num. all: 23947 / Num. obs: 23947 / % possible obs: 98.91 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1506 / % possible all: 89.32

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.01 Å / D res low: 50 Å / FOM : 0.168 / FOM acentric: 0.177 / FOM centric: 0 / Reflection: 23729 / Reflection acentric: 22468 / Reflection centric: 1261
Phasing MAD setR cullis acentric: 1.62 / R cullis centric: 1 / Highest resolution: 2.01 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 22468 / Reflection centric: 1261
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.55-501.740.30.17728
7.17-12.551.470.30.238258
5.02-7.172.190.30.1925102
3.86-5.021.180.20.11719142
3.14-3.861.20.10.12748177
2.64-3.141.73004003215
2.28-2.645.12005512254
2.01-2.282.06007102285
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se63.34233-0.11-0.804-0.0240
2Se59.75295-0.556-0.623-0.3240
3Se74.54069-0.612-0.279-0.5120
4Se85.73228-0.091-1.1530.1580
5Se74.23188-0.58-0.857-0.4730
6Se85.10638-0.089-1.3860.0150
7Se51.7496-0.356-0.828-0.2780
8Se47.3514-0.321-0.703-0.3240
9Se50.790560.107-1.3530.2310
10Se63.154790.149-1.2280.1910
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.55-500.3050.41601057728
7.17-12.550.3870.445044038258
5.02-7.170.4230.4701027925102
3.86-5.020.3150.341018611719142
3.14-3.860.2670.285029252748177
2.64-3.140.2170.228042184003215
2.28-2.640.1180.124057665512254
2.01-2.280.0510.053073877102285
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 23729
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.39-10070.60.599504
5.85-7.3965.20.81501
5.09-5.8566.80.833515
4.61-5.0962.50.861507
4.24-4.6159.90.836561
3.96-4.2464.50.84605
3.72-3.9663.80.831653
3.52-3.7263.50.812690
3.35-3.5263.30.802723
3.2-3.35660.794749
3.07-3.262.60.796775
2.96-3.0764.80.795813
2.85-2.9664.40.786846
2.76-2.8564.50.82852
2.68-2.7670.70.786921
2.6-2.6868.40.824911
2.53-2.671.10.81953
2.46-2.5369.20.7931006
2.4-2.4671.60.758988
2.34-2.4750.791055
2.29-2.34740.7991026
2.24-2.2974.70.7971084
2.2-2.2477.70.7641098
2.15-2.280.30.7431114
2.11-2.1581.50.771137
2.07-2.1183.70.7431152
2.01-2.07840.6871990

-
Processing

Software
NameVersionClassificationNB
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
DENZOdata reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→35.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.472 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.151
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1222 5.1 %RANDOM
Rwork0.162 ---
all0.164 22725 --
obs0.164 22725 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.04 Å2
2--1.84 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 20 188 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222845
X-RAY DIFFRACTIONr_bond_other_d0.0010.021859
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9463884
X-RAY DIFFRACTIONr_angle_other_deg0.95634570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65424.885131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58315496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4631515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_nbd_refined0.2070.2630
X-RAY DIFFRACTIONr_nbd_other0.1860.21871
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21405
X-RAY DIFFRACTIONr_nbtor_other0.0880.21313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3410.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.221
X-RAY DIFFRACTIONr_mcbond_it1.2191.52162
X-RAY DIFFRACTIONr_mcbond_other0.2321.5674
X-RAY DIFFRACTIONr_mcangle_it1.43622819
X-RAY DIFFRACTIONr_scbond_it2.45731265
X-RAY DIFFRACTIONr_scangle_it3.6794.51061
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 89 -
Rwork0.184 1508 -
all-1597 -
obs--89.32 %
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)
12.21890.2150.36921.4310.63921.5569-0.0947-0.40120.02950.09680.01030.04930.0784-0.1140.0844-0.09880.03040.002-0.02460.0028-0.098323.34014.622711.288
21.6251-0.4161-0.23921.9756-1.09882.50830.07670.23740.22880.0207-0.1196-0.1028-0.29550.1490.0429-0.082-0.01140.0022-0.02120.0296-0.0963-3.810330.647919.1918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1693 - 172
2X-RAY DIFFRACTION2BB0 - 1693 - 172

+
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