[English] 日本語
Yorodumi
- PDB-2rhc: Actinorhodin ketordeuctase, actKR, with NADP+ and Inhibitor Emodin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rhc
TitleActinorhodin ketordeuctase, actKR, with NADP+ and Inhibitor Emodin
ComponentsActinorhodin Polyketide Ketoreductase
KeywordsOXIDOREDUCTASE / polyketide / actinorhodin / ketoreductase / combinatorial biosynthesis / short chain dehydrogenase/reductase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / antibiotic biosynthetic process / oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKorman, T.P. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2008
Title: Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase
Authors: Korman, T.P. / Tan, Y.H. / Wong, J. / Luo, R. / Tsai, S.-C.
History
DepositionOct 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Actinorhodin Polyketide Ketoreductase
A: Actinorhodin Polyketide Ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9615
Polymers58,2042
Non-polymers1,7573
Water5,891327
1
B: Actinorhodin Polyketide Ketoreductase
A: Actinorhodin Polyketide Ketoreductase
hetero molecules

B: Actinorhodin Polyketide Ketoreductase
A: Actinorhodin Polyketide Ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,92210
Polymers116,4084
Non-polymers3,5146
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area17900 Å2
ΔGint-71 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.875, 103.875, 123.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Actinorhodin Polyketide Ketoreductase / E.C.1.3.1.- / ketoacyl reductase


Mass: 29101.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: actIII / Plasmid: pYT284 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P16544, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN / Emodin


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.8-4.8 M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2006 / Details: Vertical focusing mirror
RadiationMonochromator: Si(311) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.25 Å / Num. all: 45350 / Num. obs: 43997 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 19.7 Å2 / Limit h max: 42 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 58 / Limit l min: 0 / Observed criterion F max: 144507.78 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.077 / Net I/σ(I): 30.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 5.3 / Num. unique all: 4478 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.25 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4370 10.1 %random
Rwork0.186 ---
all-45392 --
obs-43437 95.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 64.5891 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 101.67 Å2 / Biso mean: 36.7 Å2 / Biso min: 17.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2--3.18 Å20 Å2
3----6.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 116 327 4293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.20.241513100.21545940.0115628510790.7
2.2-2.310.2275069.90.19646240.015630513091.1
2.31-2.460.218528100.19247260.0095589525494
2.46-2.650.2445349.90.20148370.0115645537195.1
2.65-2.910.2585389.90.21749080.0115638544696.6
2.91-3.330.22756510.10.20550380.015669560398.8
3.33-4.20.18360710.70.1650710.0075719567899.3
4.2-42.250.25799.90.17552690.0085914584898.9

+
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