[English] 日本語
Yorodumi
- PDB-3ez0: Crystal structure of protein of unknown function with ferritin-li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ez0
TitleCrystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution
Componentsuncharacterized protein with ferritin-like fold
Keywordsstructural genomics / unknown function / YP_832262.1 / protein of unknown function with ferritin-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Unknown ligand / Hydroxylase
Similarity search - Component
Biological speciesArthrobacter sp. FB24 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein with ferritin-like fold
B: uncharacterized protein with ferritin-like fold
C: uncharacterized protein with ferritin-like fold
D: uncharacterized protein with ferritin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,51410
Polymers101,3024
Non-polymers2126
Water3,117173
1
A: uncharacterized protein with ferritin-like fold
B: uncharacterized protein with ferritin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8636
Polymers50,6512
Non-polymers2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-14 kcal/mol
Surface area19770 Å2
MethodPISA
2
C: uncharacterized protein with ferritin-like fold
D: uncharacterized protein with ferritin-like fold


Theoretical massNumber of molelcules
Total (without water)50,6514
Polymers50,6512
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-19 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.600, 96.710, 71.200
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1112BB14 - 3414 - 34
2112DD14 - 3414 - 34
1212BB46 - 14346 - 143
2212DD46 - 14346 - 143
1313BB144 - 153144 - 153
2313DD144 - 153144 - 153
1412BB156 - 182156 - 182
2412DD156 - 182156 - 182
1512BB201 - 222201 - 222
2512DD201 - 222201 - 222
1122AA14 - 3414 - 34
2122CC14 - 3414 - 34
1222AA46 - 14346 - 143
2222CC46 - 14346 - 143
1323AA144 - 153144 - 153
2323CC144 - 153144 - 153
1422AA156 - 182156 - 182
2422CC156 - 182156 - 182
1522AA201 - 222201 - 222
2522CC201 - 222201 - 222

NCS ensembles :
ID
1
2

-
Components

#1: Protein
uncharacterized protein with ferritin-like fold


Mass: 25325.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. FB24 (bacteria) / Gene: YP_832262.1, Arth_2783 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JYP2
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.47
Details: 20.0% polyethylene glycol 3350, 0.171M potassium sodium tartrate, 0.1M MES pH 6.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 11, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.33→29.54 Å / Num. obs: 35863 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.65 % / Biso Wilson estimate: 46.71 Å2 / Rmerge F obs: 0.191 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.083 / Net I/σ(I): 10.67 / Num. measured all: 202485
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.33-2.411.0230.6121.8519518685565930.75596.2
2.41-2.510.7770.4662.420906734570870.57596.5
2.51-2.620.6350.367319609685166370.45396.9
2.62-2.760.460.2714.120349713569270.33497.1
2.76-2.930.3170.1845.720123700668240.22797.4
2.93-3.160.2180.1258.220747723670620.15597.6
3.16-3.480.1230.0712.620419712169730.08797.9
3.48-3.980.0650.04418.920127705568870.05497.6
3.98-50.0450.03223.420173702369150.0498.5
5-29.540.0390.02925.920514718270470.03698.1

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→29.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 19.064 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.507 / ESU R Free: 0.279
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. L(+)-TARTARIC ACID (TLA) IS PRESENT IN CRYSTALLIZATION CONDITION. 5. UNKNOWN LIGANDS (UNL) WERE MODELED TO ACCOUNT FOR DENSITIES NEAR THE PUTATIVE ACTIVE SITES. THEY RESEMBLE 1-ACYL-GLYCERONE-3-PHOSPHATE. ANOTHER WEAK PEG-LIKE DENSITY NEARBY WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1786 5 %RANDOM
Rwork0.21 34056 --
obs0.213 35842 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.98 Å2 / Biso mean: 46.715 Å2 / Biso min: 22.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.18 Å2
2---0.34 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.33→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 98 173 6854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226794
X-RAY DIFFRACTIONr_bond_other_d0.0020.024651
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9669170
X-RAY DIFFRACTIONr_angle_other_deg0.941311146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5925837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16421.746315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.173151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6971579
X-RAY DIFFRACTIONr_chiral_restr0.070.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021547
X-RAY DIFFRACTIONr_nbd_refined0.2020.21691
X-RAY DIFFRACTIONr_nbd_other0.1850.24652
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23391
X-RAY DIFFRACTIONr_nbtor_other0.0890.23514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.25
X-RAY DIFFRACTIONr_mcbond_it1.65734315
X-RAY DIFFRACTIONr_mcbond_other0.37131718
X-RAY DIFFRACTIONr_mcangle_it2.74956643
X-RAY DIFFRACTIONr_scbond_it4.67982796
X-RAY DIFFRACTIONr_scangle_it6.645112527
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1032TIGHT POSITIONAL0.040.05
1B1213MEDIUM POSITIONAL0.280.25
1B89LOOSE POSITIONAL0.61
1B1032TIGHT THERMAL0.311
1B1213MEDIUM THERMAL0.712
1B89LOOSE THERMAL1.9910
2A1056TIGHT POSITIONAL0.030.05
2A1193MEDIUM POSITIONAL0.210.25
2A89LOOSE POSITIONAL0.281
2A1056TIGHT THERMAL0.281
2A1193MEDIUM THERMAL0.722
2A89LOOSE THERMAL2.7610
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 145 -
Rwork0.27 2489 -
all-2634 -
obs--99.51 %
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)
11.31370.636-0.57132.078-0.34690.7924-0.0850.16110.0978-0.22040.0841-0.16250.04960.06570.0009-0.1066-0.0410.0331-0.0662-0.0007-0.10194.715983.5564.6258
22.3319-0.51540.16731.9836-0.80511.9178-0.1551-0.16540.20870.24890.077-0.2414-0.25590.09170.0781-0.06670.0047-0.045-0.0811-0.0537-0.05324.936282.613497.2549
32.2434-0.39691.06871.4461-0.17952.452-0.0911-0.69240.07720.18670.12660.02080.0003-0.5677-0.0355-0.13180.03060.01250.1667-0.0121-0.1418-15.755882.18339.7377
41.32910.49720.00882.510.26890.8141-0.08570.11680.0305-0.27640.07320.1145-0.0416-0.16360.0126-0.0746-0.0077-0.0137-0.07290.0342-0.113-16.53182.71347.9384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 223
2X-RAY DIFFRACTION2B4 - 223
3X-RAY DIFFRACTION3C11 - 223
4X-RAY DIFFRACTION4D5 - 223

+
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