[English] 日本語
Yorodumi
- PDB-3bl4: Crystal structure of a protein with unknown function (arth_0117) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bl4
TitleCrystal structure of a protein with unknown function (arth_0117) from arthrobacter sp. fb24 at 2.20 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyyp_829618.1 fold / yp_829618.1 domain like / yp_829618.1 like domains / Ribonuclease HI; Chain A / 3-Layer(aba) Sandwich / Alpha Beta / STAS/SEC14 domain-containing protein
Function and homology information
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_829618.1) from Arthrobacter sp. FB24 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _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 1.4Jan 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 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.

-
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)27,1619
Polymers26,5572
Non-polymers6047
Water1,47782
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.373, 56.127, 106.335
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 12 - 62 / Label seq-ID: 13 - 63

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

-
Components

#1: Protein Uncharacterized protein


Mass: 13278.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: FB24 / Gene: YP_829618.1, Arth_0117 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JR48
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.8
Details: NANODROP, 1.86M Ammonium sulfate, 0.2M Lithium sulfate, 0.1M CAPS pH 10.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97966
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979661
ReflectionResolution: 2.2→29.975 Å / Num. obs: 11329 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.92 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.263.50.4171.828067990.417100
2.26-2.323.50.378228668100.378100
2.32-2.393.50.3482.226597630.348100
2.39-2.463.50.3142.427027700.314100
2.46-2.543.50.253325567300.253100
2.54-2.633.50.2153.624286920.215100
2.63-2.733.50.2113.525117170.211100
2.73-2.843.50.1784.222276380.178100
2.84-2.973.50.1365.622866580.136100
2.97-3.113.50.116.520936040.11100
3.11-3.283.50.0868.520215820.086100
3.28-3.483.50.0719.719405600.071100
3.48-3.723.40.05711.317425140.057100
3.72-4.023.40.05910.916894970.059100
4.02-4.43.40.05410.915814630.054100
4.4-4.923.30.04713.713724110.047100
4.92-5.683.30.051212603820.05100
5.68-6.963.20.05510.810463280.055100
6.96-9.8430.03717.77572550.037100
9.84-29.9752.80.03713.34291560.03796.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.975 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.382 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.239
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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. SULFATE (SO4) AND ETHYLENE GLYCOL (EDO) ARE MODELED BASED ON THE CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1104 9.8 %RANDOM
Rwork0.184 ---
obs0.19 11284 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--2.24 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 33 82 1802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221771
X-RAY DIFFRACTIONr_bond_other_d0.0010.021162
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9822419
X-RAY DIFFRACTIONr_angle_other_deg0.84932824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.22122.18864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4771517
X-RAY DIFFRACTIONr_chiral_restr0.0570.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_nbd_refined0.1840.2362
X-RAY DIFFRACTIONr_nbd_other0.1940.21145
X-RAY DIFFRACTIONr_nbtor_refined0.170.2873
X-RAY DIFFRACTIONr_nbtor_other0.0870.2943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0430.25
X-RAY DIFFRACTIONr_mcbond_it1.51831206
X-RAY DIFFRACTIONr_mcbond_other0.3283476
X-RAY DIFFRACTIONr_mcangle_it2.47351857
X-RAY DIFFRACTIONr_scbond_it4.2178644
X-RAY DIFFRACTIONr_scangle_it5.62911559
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
289TIGHT POSITIONAL0.070.1
277MEDIUM POSITIONAL0.430.5
289TIGHT THERMAL0.411.2
277MEDIUM THERMAL1.243
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 84 -
Rwork0.225 713 -
all-797 -
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)
11.17750.7034-0.02940.8379-1.02472.4293-0.0788-0.1047-0.06870.0168-0.0117-0.04530.09650.11220.0904-0.0310.00670.0013-0.08070.0226-0.033611.8329-0.301424.5292
21.17840.14930.39320.6703-1.5534.53070.0520.06660.02620.0780.00760.1055-0.1565-0.0257-0.0596-0.01690.0042-0.0008-0.0728-0.003-0.03564.21417.5618-0.8386
30.4128-0.02850.34341.3701-0.68446.81750.0547-0.0189-0.20010.0235-0.1017-0.08670.4758-0.07380.0470.0157-0.0043-0.006-0.0787-0.0105-0.0077.0031-1.2658-3.2359
42.20511.256-0.31661.2119-0.50223.17820.0754-0.03160.19710.07510.0290.012-0.2542-0.079-0.1044-0.00010.025-0.0199-0.11640.0261-0.01528.21599.212121.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 745 - 75
2X-RAY DIFFRACTION2AA75 - 12376 - 124
3X-RAY DIFFRACTION3BB12 - 7413 - 75
4X-RAY DIFFRACTION4BB75 - 12376 - 124

+
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