[English] 日本語
Yorodumi
- PDB-2it9: Crystal structure of a protein with unknown function from DUF155 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2it9
TitleCrystal structure of a protein with unknown function from DUF155 family (YP_292156.1) from Prochlorococcus sp. NATL2A at 1.80 A resolution
ComponentsHypothetical protein
KeywordsStructural Genomics/Unknown function / YP_292156.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Protein of unknown function DUF1818 / Domain of unknown function (DUF1818) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Uncharacterized protein
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_292156.1) from Prochlorococcus sp. NATL2A at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,04213
Polymers60,1854
Non-polymers8569
Water6,954386
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4916
Polymers30,0932
Non-polymers3984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5517
Polymers30,0932
Non-polymers4595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.723, 81.021, 124.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLEUAA4 - 915 - 92
21LYSLEUBB4 - 915 - 92
31LYSLEUCC4 - 915 - 92
41LYSLEUDD4 - 915 - 92
52GLYSERAA100 - 119101 - 120
62GLYSERBB100 - 119101 - 120
72GLYSERCC100 - 119101 - 120
82GLYSERDD100 - 119101 - 120
DetailsSIZE EXCLUSION CHROMATOGRAPHY AND STATIC SUPPORT THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Hypothetical protein


Mass: 15046.345 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Strain: NATL2A / Gene: YP_292156.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46J75

-
Non-polymers , 5 types, 395 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 1.0M LiCl, 10.0% PEG-6000, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9740, 0.9800, 0.9799
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2006
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9741
20.981
30.97991
ReflectionResolution: 1.8→67.884 Å / Num. obs: 56456 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.853.60.6651.11481340970.665100
1.85-1.93.60.5111.41463040450.51199.9
1.9-1.953.60.35121425039310.351100
1.95-2.013.60.23931366938000.239100
2.01-2.083.60.2053.41343937160.20599.9
2.08-2.153.60.1554.51293635840.155100
2.15-2.233.60.135.41243934480.13100
2.23-2.323.60.11761199733420.117100
2.32-2.433.60.17.11148332030.199.9
2.43-2.553.60.08881100530730.088100
2.55-2.683.60.0759.31043829290.07599.9
2.68-2.853.60.06310.7985627750.06399.7
2.85-3.043.50.05411.7920525930.05499.8
3.04-3.293.50.04612.6854824400.04699.5
3.29-3.63.50.04412.9781322370.04499.2
3.6-4.023.40.03914.6687520250.03998.7
4.02-4.653.20.03218.1572517730.03297.6
4.65-5.693.50.03316.8536715330.03398.7
5.69-8.053.60.03416.3433412130.03498.3
8.05-67.883.40.03213.523716990.03296.3

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→67.884 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.666 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3) 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 4) ELECTRON DENSITY BETWEEN RESIDUES 94-96 ON CHAIN A WERE DISORDERED; THEREFORE THESE RESIDUES WERE NOT MODELED INTO THE STRUCTURE. 5) THREE MOLECULES OF TRIETHYLENE GLYCOL (PGE) USED AS A CRYOPROTECTANT (PEG-200), FOUR MOLECULES OF ETHYLENE GLYCOL (CRYOPROTECTANT); ONE MOLECULE OF TRIS HYDROXYMETHYLAMINOMETHANE (TRS); AND A CHLORIDE ANION FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2857 5.1 %RANDOM
Rwork0.179 ---
obs0.181 56272 99.29 %-
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: 33.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 51 386 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224187
X-RAY DIFFRACTIONr_bond_other_d0.0020.023864
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9495685
X-RAY DIFFRACTIONr_angle_other_deg0.92338952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9145527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.17423.861202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70915748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7691535
X-RAY DIFFRACTIONr_chiral_restr0.0920.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_nbd_refined0.2140.3717
X-RAY DIFFRACTIONr_nbd_other0.1780.33921
X-RAY DIFFRACTIONr_nbtor_refined0.1810.51969
X-RAY DIFFRACTIONr_nbtor_other0.0880.52546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5486
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.394
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.534
X-RAY DIFFRACTIONr_mcbond_it2.03132563
X-RAY DIFFRACTIONr_mcbond_other0.68731027
X-RAY DIFFRACTIONr_mcangle_it2.83954004
X-RAY DIFFRACTIONr_scbond_it4.48181948
X-RAY DIFFRACTIONr_scangle_it6.644111660
Refine LS restraints NCS

Ens-ID: 1 / Number: 1437 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.410.5
2BMEDIUM POSITIONAL0.450.5
3CMEDIUM POSITIONAL0.380.5
4DMEDIUM POSITIONAL0.460.5
1AMEDIUM THERMAL1.192
2BMEDIUM THERMAL1.022
3CMEDIUM THERMAL1.042
4DMEDIUM THERMAL0.952
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 208 -
Rwork0.275 3759 -
obs-3967 96.92 %
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)
13.76840.1849-0.91441.3444-0.38663.24010.0422-0.09930.32970.01740.01540.02-0.28790.0078-0.0576-0.25730.0066-0.0268-0.19330.0103-0.161327.573717.88731.8158
22.6589-1.5635-0.10214.0464-1.27533.5781-0.01070.1665-0.2626-0.4785-0.03170.14070.6059-0.12840.0423-0.06-0.02180.0193-0.1656-0.028-0.18332.4218-4.6087-7.7874
31.3916-0.88840.10342.21191.40814.592-0.04280.04320.1532-0.05780.1427-0.2277-0.23770.4115-0.1-0.11330.0042-0.0277-0.1537-0.0005-0.142142.97520.630531.864
42.776-1.53311.44912.3906-0.33113.3247-0.0255-0.1432-0.18190.01160.06230.34080.258-0.2967-0.0368-0.1174-0.0537-0.0056-0.1749-0.0089-0.152421.810629.628642.1551
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1221 - 123
22BB1 - 1202 - 121
33CC1 - 1202 - 121
44DD1 - 1222 - 123

+
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