[English] 日本語
Yorodumi
- PDB-6b2u: Crystal structure of Xanthomonas campestris OleA H285N with Cerulenin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b2u
TitleCrystal structure of Xanthomonas campestris OleA H285N with Cerulenin
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Thiolase / OleA / Condensation / Cerulenin
Function / homology
Function and homology information


acyl-CoA:acyl-CoA alkyltransferase / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CER / : / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJensen, M.R. / Goblirsch, B.R. / Esler, M.A. / Christenson, J.K. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008700 United States
BioTechnology Institute1000014885 10866 MNT11 United States
CitationJournal: To be published
Title: The role of OleA His285 in substrate coordination of long-chain acyl-CoA
Authors: Jensen, M.R. / Goblirsch, B.R. / Esler, M.A. / Christenson, J.K. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[ACP] synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0993
Polymers38,8181
Non-polymers2802
Water48627
1
A: 3-oxoacyl-[ACP] synthase III
hetero molecules

A: 3-oxoacyl-[ACP] synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1976
Polymers77,6372
Non-polymers5604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5300 Å2
ΔGint-17 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.516, 90.516, 69.793
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein 3-oxoacyl-[ACP] synthase III


Mass: 38818.402 Da / Num. of mol.: 1 / Mutation: H285N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: fabH, XCC0212 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PDX2
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN


Mass: 225.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antifungal, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.31 Å3/Da / Density % sol: 42.15 % / Mosaicity: 0.28 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 4000, 105 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2015
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.04→29.51 Å / Num. obs: 20876 / % possible obs: 99 % / Redundancy: 9.8 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.02 / Rrim(I) all: 0.064 / Net I/σ(I): 24.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.04-2.0990.77314710.7510.2640.81895.5
9.11-29.518.50.0262640.9990.0090.02896.7

-
Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
PHASER2.7.0phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S21

3s21


Resolution: 2.04→29.51 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.39 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1048 5 %RANDOM
Rwork0.1786 ---
obs0.1812 19822 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.08 Å2 / Biso mean: 50.006 Å2 / Biso min: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å2-0 Å2
2---0.17 Å20 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 2.04→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 9 27 2545
Biso mean--71.68 38.49 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192588
X-RAY DIFFRACTIONr_bond_other_d0.0010.022484
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9693507
X-RAY DIFFRACTIONr_angle_other_deg0.67335742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5235335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50524.299107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92915446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.351518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022895
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02501
LS refinement shellResolution: 2.045→2.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 77 -
Rwork0.258 1306 -
all-1383 -
obs--90.04 %
Refinement TLS params.Method: refined / Origin x: 42.2706 Å / Origin y: -0.802 Å / Origin z: -3.635 Å
111213212223313233
T0.1354 Å2-0.0661 Å2-0.0375 Å2-0.0593 Å20.0121 Å2--0.0182 Å2
L0.5029 °20.2679 °2-0.0455 °2-1.1088 °2-0.6206 °2--0.3764 °2
S-0.1433 Å °0.067 Å °0.0346 Å °-0.2511 Å °0.2017 Å °0.1026 Å °0.1213 Å °-0.0992 Å °-0.0585 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