[English] 日本語
Yorodumi
- PDB-5c3o: Crystal structure of the C-terminal truncated Neurospora crassa T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c3o
TitleCrystal structure of the C-terminal truncated Neurospora crassa T7H (NcT7HdeltaC) in apo form
ComponentsThymine dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / apo form / DSBH fold
Function / homology
Function and homology information


small molecule biosynthetic process / : / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding
Similarity search - Function
B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLi, W. / Zhang, T. / Ding, J.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2011CB966301 China
Ministry of Science and Technology of China2013CB910404 China
National Natural Science Foundation of China31221001 China
Chinese Academy of SciencesXDB08010302 China
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi
Authors: Li, W. / Zhang, T. / Ding, J.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3268
Polymers34,9141
Non-polymers4127
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.148, 119.148, 56.631
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Thymine dioxygenase


Mass: 34913.586 Da / Num. of mol.: 1 / Fragment: UNP residues 1-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: NCU06416 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: Q7RYZ9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M (NH4)2SO4, 0.1 M MES, 30%(W/v) PEGMME 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20591 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.555 / Net I/av σ(I): 29.2 / Net I/σ(I): 11.5 / Num. measured all: 217111
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.3810.60.54520620.895100
2.38-2.4810.70.40820300.96100
2.48-2.5910.70.31620431.042100
2.59-2.7310.70.24220231.149100
2.73-2.910.70.17320521.243100
2.9-3.1210.60.1220601.495100
3.12-3.4410.60.09720541.637100
3.44-3.9310.50.09920572.354100
3.93-4.9510.40.09320762.428100
4.95-50100.05721342.38399.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
SADABSphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.928 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1053 5.1 %RANDOM
Rwork0.1964 ---
obs0.1978 19527 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.55 Å2 / Biso mean: 50.323 Å2 / Biso min: 24.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.16 Å20 Å2
2--0.16 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 25 109 2183
Biso mean--71.96 53.96 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192119
X-RAY DIFFRACTIONr_bond_other_d00.021996
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9632862
X-RAY DIFFRACTIONr_angle_other_deg3.55834601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42624.608102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62215326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2331510
X-RAY DIFFRACTIONr_chiral_restr0.060.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212386
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02484
X-RAY DIFFRACTIONr_mcbond_it1.8884.2381036
X-RAY DIFFRACTIONr_mcbond_other1.8884.2361035
X-RAY DIFFRACTIONr_mcangle_it3.3696.321288
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 86 -
Rwork0.217 1424 -
all-1510 -
obs--99.41 %
Refinement TLS params.Method: refined / Origin x: 15.8585 Å / Origin y: 48.9611 Å / Origin z: 31.6384 Å
111213212223313233
T0.0313 Å20.0183 Å2-0.011 Å2-0.0242 Å20.0025 Å2--0.0225 Å2
L1.6527 °2-0.7933 °20.7389 °2-0.667 °2-0.4464 °2--0.8535 °2
S-0.0014 Å °-0.1053 Å °-0.1704 Å °0.0012 Å °0.0847 Å °0.0799 Å °0.0705 Å °-0.0473 Å °-0.0832 Å °

+
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