[English] 日本語
Yorodumi
- PDB-5bux: Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Ye... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bux
TitleCrystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
KeywordsLYASE / FabZ / antimicrobial target / hot-dog fold / fatty acid synthesis / trimer of dimers
Function / homology
Function and homology information


(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesYersinia pestis KIM10+ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMcGillick, B. / Kumaran, D. / Swaminathan, S.
CitationJournal: To be Published
Title: Crystal Structure of 3-hydroxyacyl-ACP dehydratase (FabZ) from Yersinia pestis with glycerol bound
Authors: McGillick, B. / Kumaran, D. / Swaminathan, S.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0147
Polymers42,6562
Non-polymers3585
Water3,693205
1
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
hetero molecules

A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
hetero molecules

A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,04221
Polymers127,9676
Non-polymers1,07515
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19430 Å2
ΔGint-123 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.760, 104.760, 87.961
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxymyristoyl-ACP dehydrase / ...(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxymyristoyl-ACP dehydrase / Beta-hydroxyacyl-ACP dehydratase


Mass: 21327.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis KIM10+ (bacteria) / Strain: KIM10+ / Gene: fabZ, YPA_0531 / Plasmid: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1CAM3, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% Tacsimate, pH 8.0, 400 mM sodium thiocyanate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 42366 / Num. obs: 42366 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.3
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 2 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZHG

1zhg


Resolution: 1.9→39.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.852 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18534 2140 5.1 %RANDOM
Rwork0.15543 ---
obs0.15691 40206 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.46 Å2-0 Å2
2--0.46 Å2-0 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 21 205 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192349
X-RAY DIFFRACTIONr_bond_other_d0.0010.022306
X-RAY DIFFRACTIONr_angle_refined_deg2.3641.9783157
X-RAY DIFFRACTIONr_angle_other_deg0.99835302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05522.593108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3951520
X-RAY DIFFRACTIONr_chiral_restr0.1660.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 126 -
Rwork0.191 2528 -
obs--83.51 %

+
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