[English] 日本語
Yorodumi
- PDB-4f32: Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f32
TitleCrystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II from Burkholderia vietnamiensis in complex with platencin
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Unknown peptide
KeywordsTransferase/Antibiotic / SSGCID / 3-oxoacyl-[acyl-carrier-protein] synthase II / platencin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Antibiotic complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N32 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
Streptomyces platensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8567
Polymers93,8813
Non-polymers9754
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-45 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.490, 100.840, 143.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a dimer, same as the asymmetric unit

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 46803.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (bacteria) / Strain: G4/LMG 22486 / Gene: Bcep1808_4002 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4JL30, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Protein/peptide Unknown peptide


Mass: 273.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: from a strain of S. platensis, MA7339, recovered from a soil sample collected in Minut II (Mallorca) in Spain, Proc Natl Acad Sci U S A. 2007 May 1;104(18):7612-6
Source: (synth.) Streptomyces platensis (bacteria)
#3: Chemical ChemComp-N32 / 2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid / Platencin


Mass: 425.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27NO6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MD Morpheus a2: 10% PEG 8000, 20% Ethylene glycol, 30mM MgCl2, 30mM CaCl2, 100mM MES/Imidazole 6.5, BuviA.00113.b.A1 PS01317 at 20mg/ml with 1mM Platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 3, 2012 / Details: RIGAKU VARIMAX HF
RadiationMonochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 64282 / Num. obs: 63570 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.4 % / Biso Wilson estimate: 16.926 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 27.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.956.30.3345.6927540437392.8
1.95-29.80.2699.1542449434595.7
2-2.0612.30.22312.5353460435297.2
2.06-2.1213.60.18915.3458080426799.2
2.12-2.1915.10.17118.1963459419599.8
2.19-2.2716.40.15820.55663484053100
2.27-2.3617.60.14222.97694333940100
2.36-2.4520.10.13825.21760273783100
2.45-2.5621.60.12927.31785993635100
2.56-2.6921.70.11828.83752023469100
2.69-2.8321.70.10630.61720653322100
2.83-321.80.09732.99684033141100
3-3.2121.80.08735.75646962975100
3.21-3.4721.70.07541.55603522780100
3.47-3.821.40.06549.95542742534100
3.8-4.2521.30.05955.61500722350100
4.25-4.9121.30.05655.96438142057100
4.91-6.0121.30.06246.57379201777100
6.01-8.520.90.05746.0829241140099.9
8.518.80.04556.991547382298.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.97 Å
Translation3.5 Å19.97 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1538 / WRfactor Rwork: 0.1238 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9207 / SU B: 4.133 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1249 / SU Rfree: 0.1126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 3215 5.1 %RANDOM
Rwork0.1374 ---
obs0.1391 63570 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.26 Å2 / Biso mean: 10.1563 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2--0.1 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 70 816 6955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196367
X-RAY DIFFRACTIONr_bond_other_d0.0010.024275
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9888678
X-RAY DIFFRACTIONr_angle_other_deg0.982310410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97923.089246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79415952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4491554
X-RAY DIFFRACTIONr_chiral_restr0.0930.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217375
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021307
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 229 -
Rwork0.192 3898 -
all-4127 -
obs--92.24 %
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)
10.20170.0057-0.02890.26780.09210.36260.0003-0.0150.00520.03570.00060.00750.0102-0.0096-0.00090.00680.00240.0040.00390.00340.0066-16.5140.841-20.871
20.18380.0013-0.0450.26710.01280.2662-0.00560.0195-0.0008-0.02770.0138-0.0163-0.01420.0161-0.00820.0057-0.00350.00330.0051-0.00340.0061-11.152-0.59-50.349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 422
2X-RAY DIFFRACTION2B0 - 422

+
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