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- PDB-4zjb: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 4zjb
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) in complex with holo-ACP from Helicobacter pylori
Components
  • 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
  • Acyl carrier protein
KeywordsLYASE/BIOSYNTHETIC PROTEIN / FAS / Fatty acid biosynthesis / complex / LYASE-BIOSYNTHETIC PROTEIN complex
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / cytosol / 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 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site ...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 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 4'-PHOSPHOPANTETHEINE / Acyl carrier protein / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsZhang, L. / Zhang, L. / Shen, X. / Jiang, H.
CitationJournal: Cell Res. / Year: 2016
Title: Crystal structure of FabZ-ACP complex reveals a dynamic seesaw-like catalytic mechanism of dehydratase in fatty acid biosynthesis.
Authors: Zhang, L. / Xiao, J. / Xu, J. / Fu, T. / Cao, Z. / Zhu, L. / Chen, H.Z. / Shen, X. / Jiang, H. / Zhang, L.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Data collection / Derived calculations / Experimental preparation
Category: diffrn_source / exptl_crystal_grow / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,1375
Polymers48,5873
Non-polymers5502
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-37 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.705, 127.705, 127.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

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Components

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


Mass: 19611.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabZ / Production host: Escherichia coli (E. coli)
References: UniProt: Q5G940, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Protein Acyl carrier protein / ACP


Mass: 9363.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: acpP, EG63_02640, HPY173_03440, HPY1786_00110, HPY1846_06495, HPY207_02635, HPY228_03880, HPY499_02145, JM68_05695
Production host: Escherichia coli (E. coli) / References: UniProt: Q5EDC8
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 69.01 %
Crystal growMethod: vapor diffusion, hanging drop / Details: PEG 3350, sodium citrate

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 22941 / % possible obs: 99.7 % / Redundancy: 10 % / Net I/σ(I): 49.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data processing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GLL and 1L0I

2gll

1l0i


Resolution: 2.55→31.926 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2019 8.83 %
Rwork0.19 --
obs0.1936 22857 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→31.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 34 72 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013149
X-RAY DIFFRACTIONf_angle_d1.3094263
X-RAY DIFFRACTIONf_dihedral_angle_d18.4711168
X-RAY DIFFRACTIONf_chiral_restr0.049475
X-RAY DIFFRACTIONf_plane_restr0.006546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61380.28021370.23251465X-RAY DIFFRACTION99
2.6138-2.68440.27051430.22481459X-RAY DIFFRACTION100
2.6844-2.76330.26121450.21831486X-RAY DIFFRACTION100
2.7633-2.85250.26481410.22481476X-RAY DIFFRACTION100
2.8525-2.95440.24531410.22751479X-RAY DIFFRACTION100
2.9544-3.07260.27361420.22711482X-RAY DIFFRACTION100
3.0726-3.21230.29961460.22281478X-RAY DIFFRACTION100
3.2123-3.38150.27411410.22811469X-RAY DIFFRACTION100
3.3815-3.59310.26521470.2041489X-RAY DIFFRACTION100
3.5931-3.870.25621520.18721506X-RAY DIFFRACTION100
3.87-4.25870.2021440.1881484X-RAY DIFFRACTION100
4.2587-4.87310.17441470.15551499X-RAY DIFFRACTION100
4.8731-6.13240.23041500.1811523X-RAY DIFFRACTION100
6.1324-31.92870.211430.16611543X-RAY DIFFRACTION97

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