[English] 日本語
Yorodumi
- PDB-3f7x: Crystal structure of a putative polyketide cyclase (pp0894) from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f7x
TitleCrystal structure of a putative polyketide cyclase (pp0894) from pseudomonas putida kt2440 at 1.24 A resolution
ComponentsPutative polyketide cyclase
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Conserved hypothetical protein CHP02096 / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.24 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative polyketide cyclase. (NP_743055.1) from PSEUDOMONAS PUTIDA KT2440 at 1.24 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7549
Polymers17,3811
Non-polymers3728
Water3,243180
1
A: Putative polyketide cyclase
hetero molecules

A: Putative polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,50818
Polymers34,7632
Non-polymers74516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5500 Å2
ΔGint14 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.762, 74.985, 36.543
Angle α, β, γ (deg.)90.000, 118.030, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative polyketide cyclase


Mass: 17381.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: NP_743055.1, PP0894, PP_0894 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88PF6
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG, WITH THE ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG, WITH THE CRYSTALLIZED PROTEIN CONTAINING THE PURIFICATION TAG FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 1.24→40.096 Å / Num. obs: 35808 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.24-1.280.51528786294389
1.28-1.340.39314991418799.8
1.34-1.40.29412919355599.5
1.4-1.470.2185.312354337799.7
1.47-1.560.1477.412985353599.7
1.56-1.680.1069.813361362499.6
1.68-1.850.07812.713495362999.5
1.85-2.120.05616.313451364699.3
2.12-2.670.0582118277362599.5
2.67-40.0960.04429.127023368299.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0063refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.24→40.096 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 1.191 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5. TWO UN-IDENTIFIED LIGANDS (UNL 1 AND UNL 2) WERE MODELED INTO THE PUTATIVE ACTIVE SITE. 6. THE REGION SURROUNDING THE SIDECHAINS OF GLU 51 AND ARG 55 CONTAINS UNEXPLAINED DIFFERENCE ELECTRON DENSITIES THAT COULD NOT BE RELIABLY MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.15 1790 5 %RANDOM
Rwork0.12 ---
obs0.122 35806 99.01 %-
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 max: 50.65 Å2 / Biso mean: 16.437 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20.08 Å2
2--0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.24→40.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 44 180 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221192
X-RAY DIFFRACTIONr_bond_other_d0.0010.02831
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9471625
X-RAY DIFFRACTIONr_angle_other_deg0.932020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83823.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8315203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9651510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
X-RAY DIFFRACTIONr_mcbond_it2.4363712
X-RAY DIFFRACTIONr_mcbond_other1.5593290
X-RAY DIFFRACTIONr_mcangle_it3.40251150
X-RAY DIFFRACTIONr_scbond_it4.5458480
X-RAY DIFFRACTIONr_scangle_it5.94711457
X-RAY DIFFRACTIONr_rigid_bond_restr1.82932023
X-RAY DIFFRACTIONr_sphericity_free9.0623222
X-RAY DIFFRACTIONr_sphericity_bonded4.32331989
LS refinement shellResolution: 1.24→1.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 130 -
Rwork0.215 2257 -
all-2387 -
obs--88.11 %

+
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