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- PDB-4i83: Crystal Structure of (3R)-Hydroxymyristoyl-ACP Dehydratase from N... -

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Basic information

Entry
Database: PDB / ID: 4i83
TitleCrystal Structure of (3R)-Hydroxymyristoyl-ACP Dehydratase from Neisseria meningitidis FAM18
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
KeywordsLYASE / FabZ / Hot Dog Fold / thioesterase
Function / homology
Function and homology information


: / : / : / : / 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
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKhandokar, Y.B. / Forwood, J.K.
CitationJournal: To be published
Title: Crystal Structure of (3R)-Hydroxymyristoyl-ACP Dehydratase from Neisseria meningitidis FAM18
Authors: Khandokar, Y.B. / Forwood, J.K.
History
DepositionDec 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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
C: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
D: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
E: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
F: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ


Theoretical massNumber of molelcules
Total (without water)101,4226
Polymers101,4226
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-65 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.440, 103.980, 135.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23D
14A
24E
15A
25F
16C
26B
17C
27D
18C
28E
19C
29F
110B
210D
111B
211E
112B
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 146 / Label seq-ID: 6 - 149

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22BC
13AA
23DD
14AA
24EE
15AA
25FF
16CB
26BC
17CB
27DD
18CB
28EE
19CB
29FF
110BC
210DD
111BC
211EE
112BC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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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: 16903.729 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: FAM18 / Gene: fabZ, NMC0170 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3pLyse
References: UniProt: A1KRL1, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM Sodium Acetate, 7.5% PEG 4000, 10% Glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→44.73 Å / Num. all: 36282 / Num. obs: 36282 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.61 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z6B

1z6b


Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.422 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25589 1617 5 %RANDOM
Rwork0.22362 ---
obs0.22523 30575 99.69 %-
all-30670 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 0 0 6756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196840
X-RAY DIFFRACTIONr_bond_other_d0.0060.026846
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9769244
X-RAY DIFFRACTIONr_angle_other_deg1.017315752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47324.899298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0861534
X-RAY DIFFRACTIONr_chiral_restr0.0880.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217688
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021498
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90320.05
12C90320.05
21A89920.05
22B89920.05
31A90580.05
32D90580.05
41A89780.05
42E89780.05
51A90260.05
52F90260.05
61C90170.05
62B90170.05
71C90470.05
72D90470.05
81C89720.04
82E89720.04
91C90500.04
92F90500.04
101B90550.05
102D90550.05
111B89520.04
112E89520.04
121B90650.04
122F90650.04
131D90020.04
132E90020.04
141D91190.04
142F91190.04
151E89720.04
152F89720.04
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 132 -
Rwork0.316 2194 -
obs--99.91 %

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