[English] 日本語
Yorodumi
- PDB-2ozj: CRYSTAL STRUCTURE OF A CUPIN SUPERFAMILY PROTEIN (DSY2733) FROM D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ozj
TitleCRYSTAL STRUCTURE OF A CUPIN SUPERFAMILY PROTEIN (DSY2733) FROM DESULFITOBACTERIUM HAFNIENSE DCB-2 AT 1.60 A RESOLUTION
ComponentsCupin 2, conserved barrel
KeywordsUNKNOWN FUNCTION / CUPIN SUPERFAMILY PROTEIN / CUPIN 2 / CONSERVED BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cyclic nucleotide-binding protein / :
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Cupin 2, conserved barrel (EAT53321.1) from Desulfitobacterium hafniense DCB-2 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: 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: 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_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 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 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 SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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: Cupin 2, conserved barrel
B: Cupin 2, conserved barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0633
Polymers25,9702
Non-polymers921
Water2,432135
1
A: Cupin 2, conserved barrel

A: Cupin 2, conserved barrel


Theoretical massNumber of molelcules
Total (without water)25,9702
Polymers25,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2940 Å2
ΔGint-28 kcal/mol
Surface area10280 Å2
MethodPISA, PQS
2
B: Cupin 2, conserved barrel
hetero molecules

B: Cupin 2, conserved barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1554
Polymers25,9702
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3510 Å2
ΔGint-27 kcal/mol
Surface area10180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.930, 69.790, 150.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-186-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End label comp-ID: ASP / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEAA1 - 1102 - 111
22ALABB2 - 1103 - 111
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS A TRIMER IN SOLUTION. HOWEVER, THE PISA SERVER PREDICTS THE DIMER TO BE STABLE.

-
Components

#1: Protein Cupin 2, conserved barrel


Mass: 12985.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: EAT53321.1, Dhaf_2995 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q18ZY6, UniProt: B8FSC7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 0.25M Sodium chloride, 33.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97941, 0.97917
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 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
20.979411
30.979171
ReflectionResolution: 1.6→28.88 Å / Num. obs: 28987 / % possible obs: 99.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.16
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.6-1.6697.30.6752.120962197.3
1.66-1.7299.80.5262.718925199.8
1.72-1.899.70.3723.821490199.7
1.8-1.999.70.2525.522010199.7
1.9-2.0299.80.1638.321232199.8
2.02-2.1799.90.10212.420140199.9
2.17-2.391000.0716.6214241100
2.39-2.7399.80.05421.420862199.8
2.73-3.4499.60.03729.621054199.6
3.44-28.998.10.02339.220620198.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.453 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN 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 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. THE GEOMETRY OF THE SEVERAL REGIONS ARE POOR DUE TO DISORDER. THESE REGIONS ARE RESIDUES 3-5, 19-30, 47-51 AND 108-110 IN A AND B SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21269 1475 5.1 %RANDOM
Rwork0.1822 ---
obs0.18374 28943 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.049 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--1.37 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 6 135 1815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221840
X-RAY DIFFRACTIONr_bond_other_d0.0020.021226
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.9952509
X-RAY DIFFRACTIONr_angle_other_deg0.96633032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1835245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48925.13574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45515329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.374159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022074
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
X-RAY DIFFRACTIONr_nbd_refined0.2170.2277
X-RAY DIFFRACTIONr_nbd_other0.2030.21277
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2852
X-RAY DIFFRACTIONr_nbtor_other0.0890.21088
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.331246
X-RAY DIFFRACTIONr_mcbond_other0.7393470
X-RAY DIFFRACTIONr_mcangle_it3.13751916
X-RAY DIFFRACTIONr_scbond_it5.0478680
X-RAY DIFFRACTIONr_scangle_it7.41211591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1237 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.780.5
medium thermal1.412
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 92 -
Rwork0.244 1987 -
obs--97.33 %
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)
11.49260.41080.42410.5291.54218.69970.0508-0.1575-0.11420.11310.05450.01490.4950.4015-0.1053-0.04380.03370.0017-0.079-0.0116-0.07895.13132.71269.3193
20.97770.0696-0.43851.06240.1633.7894-0.05430.1749-0.1589-0.19830.01020.04970.1515-0.17820.0441-0.1031-0.02610.0002-0.1018-0.0162-0.056-2.182340.194528.3239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1102 - 111
2X-RAY DIFFRACTION2BB2 - 1103 - 111

+
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