[English] 日本語
Yorodumi
- PDB-4hzn: The Structure of the Bifunctional Acetyltransferase/Decarboxylase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hzn
TitleThe Structure of the Bifunctional Acetyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double Hot Dog Fold
ComponentsBifunctional Methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology / Double Hot Dog Fold / Bifunctional methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase / Acyl Carrier Protein (LnmK) methylmalonyl-CoA
Function / homologyS-acyltransferase activity / LnmK, N-terminal / LnmK N-terminal Hot Dog Fold domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Conserved hypthetical protein
Function and homology information
Biological speciesStreptomyces atroolivaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsLohman, J.R. / Bingman, C.A. / Phillips Jr., G.N. / Shen, B. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Biochemistry / Year: 2013
Title: Structure of the Bifunctional Acyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double-Hot-Dog Fold.
Authors: Lohman, J.R. / Bingman, C.A. / Phillips, G.N. / Shen, B.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional Methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0738
Polymers37,3791
Non-polymers6957
Water2,036113
1
A: Bifunctional Methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
hetero molecules

A: Bifunctional Methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,14716
Polymers74,7582
Non-polymers1,38914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6350 Å2
ΔGint-128 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.165, 60.165, 311.193
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Bifunctional Methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase


Mass: 37378.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atroolivaceus (bacteria) / Gene: LnmK / Plasmid: pCDF-2 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GGP1
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: Protein solution: 45 mg/mL protein in 10 mM NaCl and 10 mM Tris-HCl, 2.5 mM methylmalonyl-CoA, pH 8.0. Precipitant solution: 12 - 18% glycerol, 1.3 - 1.6 M (NH4)2SO4, 0.1 M Tris-HCl, pH 7.0 - ...Details: Protein solution: 45 mg/mL protein in 10 mM NaCl and 10 mM Tris-HCl, 2.5 mM methylmalonyl-CoA, pH 8.0. Precipitant solution: 12 - 18% glycerol, 1.3 - 1.6 M (NH4)2SO4, 0.1 M Tris-HCl, pH 7.0 - 8.5 (1:1, protein:well), VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97941, 1.127
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2009
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
21.1271
ReflectionResolution: 2.25→28.06 Å / Num. all: 17112 / Num. obs: 16907 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 28.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→28.06 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.519 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25381 869 5.2 %RANDOM
Rwork0.19977 ---
obs0.20245 15889 100 %-
all-16907 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.25→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 39 113 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9673335
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69522.131122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.911531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.51499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09822418
X-RAY DIFFRACTIONr_scbond_it1.6253949
X-RAY DIFFRACTIONr_scangle_it2.6064.5914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 67 -
Rwork0.196 1147 -
obs--100 %

+
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