[English] 日本語
Yorodumi
- PDB-5eeh: Crystal structure of carminomycin-4-O-methyltransferase DnrK in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eeh
TitleCrystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 2-chloro-4-nitrophenol
ComponentsCarminomycin 4-O-methyltransferase DnrK
KeywordsTRANSFERASE / unnatural substrate / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation
Similarity search - Function
Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-chloranyl-4-nitro-phenol / S-ADENOSYL-L-HOMOCYSTEINE / Carminomycin 4-O-methyltransferase DnrK
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWang, F. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM098248 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI52188 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways.
Authors: Huber, T.D. / Wang, F. / Singh, S. / Johnson, B.R. / Zhang, J. / Sunkara, M. / Van Lanen, S.G. / Morris, A.J. / Phillips, G.N. / Thorson, J.S.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carminomycin 4-O-methyltransferase DnrK
B: Carminomycin 4-O-methyltransferase DnrK
C: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,62230
Polymers123,0013
Non-polymers4,62127
Water16,448913
1
A: Carminomycin 4-O-methyltransferase DnrK
hetero molecules

A: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,62124
Polymers82,0012
Non-polymers3,62022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area8830 Å2
ΔGint-165 kcal/mol
Surface area25950 Å2
MethodPISA
2
B: Carminomycin 4-O-methyltransferase DnrK
hetero molecules

C: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,81218
Polymers82,0012
Non-polymers2,81116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Buried area7620 Å2
ΔGint-115 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.347, 110.678, 116.869
Angle α, β, γ (deg.)90.000, 120.240, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA11 - 1006
211chain BB13 - 1006
311chain CC11 - 1003

-
Components

#1: Protein Carminomycin 4-O-methyltransferase DnrK / COMT / Anthracycline 4-O-methyltransferase


Mass: 41000.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dnrK / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q06528, carminomycin 4-O-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-P9P / 2-chloranyl-4-nitro-phenol


Mass: 173.554 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H4ClNO3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.26M (NH4)SO4, 0.1M Tris pH 8.0, 0.2M Li2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→48.5 Å / Num. all: 578485 / Num. obs: 235152 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.46 % / Biso Wilson estimate: 21.17 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.08 / Rsym value: 0.071 / Χ2: 1.002 / Net I/σ(I): 10.53 / Num. measured all: 695966
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.82-1.8652.330.520.4132.784467456152311981.00692.3
1.71-1.820.7560.4631.497310452782433520.6182.1
1.82-1.970.8960.2913.0711347149252485210.37698.5
1.97-2.160.9610.1595.6611087445092448310.20499.4
2.16-2.410.9820.0968.910088840919405990.12399.2
2.41-2.780.990.06712.318914036113357590.08699
2.78-3.410.9930.0516.727491530476300690.06498.7
3.41-4.80.9940.04121.585746323592230610.05397.7
4.80.9940.03922.863143713080126430.0596.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEG

5eeg


Resolution: 1.82→48.5 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 1974 1.65 %Random selection
Rwork0.1544 117392 --
obs0.1549 119366 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.9 Å2 / Biso mean: 32.4476 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.82→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7918 0 288 913 9119
Biso mean--33.59 41.69 -
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078527
X-RAY DIFFRACTIONf_angle_d1.11811652
X-RAY DIFFRACTIONf_chiral_restr0.0461310
X-RAY DIFFRACTIONf_plane_restr0.0051528
X-RAY DIFFRACTIONf_dihedral_angle_d12.2593092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4805X-RAY DIFFRACTION3.88TORSIONAL
12B4805X-RAY DIFFRACTION3.88TORSIONAL
13C4805X-RAY DIFFRACTION3.88TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.86550.24741330.22197809794292
1.8655-1.9160.25051420.19538255839797
1.916-1.97230.24111220.18038256837897
1.9723-2.0360.2081470.16818317846498
2.036-2.10880.19431410.16318371851299
2.1088-2.19320.18731440.16078376852099
2.1932-2.2930.19921400.15358453859399
2.293-2.41390.19131450.15668430857599
2.4139-2.56510.20541420.154684808622100
2.5651-2.76320.18321470.159284798626100
2.7632-3.04120.19881430.160984798622100
3.0412-3.48120.19641430.155585278670100
3.4812-4.38550.13821440.130185448688100
4.3855-48.54480.16831410.143886168757100
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)
10.61740.06230.44730.3031-0.05011.18980.036-0.09140.00620.0685-0.0226-0.0633-0.10980.1177-0.00840.1088-0.01970.01690.1112-0.01240.132377.145228.7529115.0895
20.73250.32820.45050.6501-0.03041.12580.031-0.007-0.0996-0.04530.05010.02420.1041-0.0725-0.07740.1323-0.04080.01520.13940.02970.1828104.121151.2115118.2218
30.49630.2660.11581.27561.23231.4491-0.00990.2256-0.0416-0.6107-0.1790.225-0.442-0.22940.10970.41450.1648-0.09630.3368-0.08070.230971.628859.4978152.3874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 11 through 407)A0
2X-RAY DIFFRACTION2(chain 'B' and resid 13 through 407)B0
3X-RAY DIFFRACTION3(chain 'C' and resid 11 through 404)C0

+
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