PDB-3d6x: Crystal structure of Campylobacter jejuni FabZ

ID or keywords:

Entry

Database: PDB / ID: 3d6x

Title

Crystal structure of Campylobacter jejuni FabZ

Components

(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

Keywords

LYASE / FabZ / hot dog fold / dehydratase / Campylobacter jejuni / Lipid A biosynthesis / Lipid synthesis

Function / homology

Function and homology information

: / : / : / : / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.59 Å

Authors

Yokoyama, T. / Yeo, H.J.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Campylobacter jejuni fatty acid synthase II: structural and functional analysis of beta-hydroxyacyl-ACP dehydratase (FabZ).
Authors: Kirkpatrick, A.S. / Yokoyama, T. / Choi, K.J. / Yeo, H.J.

History

Deposition	May 20, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 5, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3d6x.cif.gz	170.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3d6x_validation.pdf.gz	477.6 KB	Display	wwPDB validaton report
Full document	3d6x_full_validation.pdf.gz	513.6 KB	Display
Data in XML	3d6x_validation.xml.gz	33 KB	Display
Data in CIF	3d6x_validation.cif.gz	44.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/3d6x ftp://data.pdbj.org/pub/pdb/validation_reports/d6/3d6x	HTTPS FTP

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Related structure data

Related structure data	2glmS S: Starting model for refinement
Similar structure data	3aza-1 3aza-4 3az9-1 3aza-2 5a9f-d 3azb-4 2bii-2 5vae-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (5)

Deposited unit

A: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

B: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

C: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

D: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

E: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

F: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

101 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.589, 93.403, 126.631
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	PHE	PHE	2	A	A	11 - 73	11 - 73
2	1	1	LEU	LEU	PHE	PHE	2	B	B	11 - 73	11 - 73
3	1	1	LEU	LEU	PHE	PHE	2	C	C	11 - 73	11 - 73
4	1	1	LEU	LEU	PHE	PHE	2	D	D	11 - 73	11 - 73
5	1	1	LEU	LEU	PHE	PHE	2	E	E	11 - 73	11 - 73
6	1	1	LEU	LEU	PHE	PHE	2	F	F	11 - 73	11 - 73
7	2	1	VAL	VAL	ALA	ALA	2	A	A	86 - 141	86 - 141
8	2	1	VAL	VAL	ALA	ALA	2	B	B	86 - 141	86 - 141
9	2	1	VAL	VAL	ALA	ALA	2	C	C	86 - 141	86 - 141
10	2	1	VAL	VAL	ALA	ALA	2	D	D	86 - 141	86 - 141
11	2	1	VAL	VAL	ALA	ALA	2	E	E	86 - 141	86 - 141
12	2	1	VAL	VAL	ALA	ALA	2	F	F	86 - 141	86 - 141
1	1	2	MSE	MSE	ILE	ILE	5	A	A	1 - 10	1 - 10
2	1	2	MSE	MSE	ILE	ILE	5	B	B	1 - 10	1 - 10
3	1	2	MSE	MSE	ILE	ILE	5	C	C	1 - 10	1 - 10
4	1	2	MSE	MSE	ILE	ILE	5	D	D	1 - 10	1 - 10
5	1	2	MSE	MSE	ILE	ILE	5	E	E	1 - 10	1 - 10
6	1	2	MSE	MSE	ILE	ILE	5	F	F	1 - 10	1 - 10
7	2	2	GLU	GLU	LYS	LYS	5	A	A	74 - 85	74 - 85
8	2	2	GLU	GLU	LYS	LYS	5	B	B	74 - 85	74 - 85
9	2	2	GLU	GLU	LYS	LYS	5	C	C	74 - 85	74 - 85
10	2	2	GLU	GLU	LYS	LYS	5	D	D	74 - 85	74 - 85
11	2	2	GLU	GLU	LYS	LYS	5	E	E	74 - 85	74 - 85
12	2	2	GLU	GLU	LYS	LYS	5	F	F	74 - 85	74 - 85
13	3	2	MSE	MSE	VAL	VAL	5	A	A	142 - 144	142 - 144
14	3	2	MSE	MSE	ASP	ASP	5	B	B	142 - 145	142 - 145
15	3	2	MSE	MSE	ASP	ASP	5	C	C	142 - 145	142 - 145
16	3	2	MSE	MSE	VAL	VAL	5	D	D	142 - 144	142 - 144
17	3	2	MSE	MSE	ASP	ASP	5	E	E	142 - 145	142 - 145
18	3	2	MSE	MSE	VAL	VAL	5	F	F	142 - 144	142 - 144

NCS ensembles :

ID
1
2

#1: Protein	(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxymyristoyl ACP dehydrase Mass: 16836.402 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter) Gene: fabZ, CJJ81176_0300 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: A1VXZ7, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxymyristoyl ACP dehydrase

Mass: 16836.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter)
Gene: fabZ, CJJ81176_0300 / Plasmid: pGEX-6P1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A1VXZ7, Lyases; Carbon-oxygen lyases; Hydro-lyases

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.57 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 14% Polyethylene glycol monomethylether 550, 0.2M NaCl, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2007
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.59→80 Å / Num. obs: 29418 / % possible obs: 88.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / R_merge(I) obs: 0.072 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.59→2.69 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.264 / % possible all: 60.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data collection
HKL-3000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2GLM

2glm

Resolution: 2.59→75.16 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.912 / SU B: 29.478 / SU ML: 0.281 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.312 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25361	1490	5.1 %	RANDOM
R_work	0.21628	-	-	-
obs	0.21823	27907	87.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 56.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.56 Å²	0 Å²	0 Å²
2-	-	-1.36 Å²	0 Å²
3-	-	-	-1.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.59→75.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6612	0	0	15	6627

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	6768
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.582	1.968	9123
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.738	5	827
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.639	24.187	289
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.105	15	1216
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.47	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	1006
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5014
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.273	0.3	2970
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.344	0.5	4568
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.5	428
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.383	0.3	23
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.421	0.5	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.128	2	4240
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.38	3	6708
X-RAY DIFFRACTION	r_scbond_it	1.073	2	2822
X-RAY DIFFRACTION	r_scangle_it	1.531	3	2415
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	476	tight positional	0.04	0.05
1	2	B	476	tight positional	0.05	0.05
1	3	C	476	tight positional	0.04	0.05
1	4	D	476	tight positional	0.04	0.05
1	5	E	476	tight positional	0.05	0.05
1	6	F	476	tight positional	0.05	0.05
1	1	A	462	medium positional	0.55	0.5
1	2	B	462	medium positional	0.59	0.5
1	3	C	462	medium positional	0.57	0.5
1	4	D	462	medium positional	0.63	0.5
1	5	E	462	medium positional	0.64	0.5
1	6	F	462	medium positional	0.58	0.5
2	1	A	68	medium positional	0.52	0.5
2	2	B	68	medium positional	0.57	0.5
2	3	C	68	medium positional	0.59	0.5
2	4	D	68	medium positional	0.45	0.5
2	5	E	68	medium positional	0.47	0.5
2	6	F	68	medium positional	0.72	0.5
2	1	A	68	loose positional	1.72	5
2	2	B	68	loose positional	1.82	5
2	3	C	68	loose positional	1.55	5
2	4	D	68	loose positional	1.25	5
2	5	E	68	loose positional	1.12	5
2	6	F	68	loose positional	1.75	5
1	1	A	476	tight thermal	0.09	0.5
1	2	B	476	tight thermal	0.11	0.5
1	3	C	476	tight thermal	0.1	0.5
1	4	D	476	tight thermal	0.08	0.5
1	5	E	476	tight thermal	0.08	0.5
1	6	F	476	tight thermal	0.08	0.5
1	1	A	462	medium thermal	0.63	2
1	2	B	462	medium thermal	0.65	2
1	3	C	462	medium thermal	0.59	2
1	4	D	462	medium thermal	0.5	2
1	5	E	462	medium thermal	0.43	2
1	6	F	462	medium thermal	0.52	2
2	1	A	68	medium thermal	0.64	2
2	2	B	68	medium thermal	0.68	2
2	3	C	68	medium thermal	0.85	2
2	4	D	68	medium thermal	0.75	2
2	5	E	68	medium thermal	0.49	2
2	6	F	68	medium thermal	0.64	2
2	1	A	68	loose thermal	1.77	10
2	2	B	68	loose thermal	2.47	10
2	3	C	68	loose thermal	1.91	10
2	4	D	68	loose thermal	1.56	10
2	5	E	68	loose thermal	2.18	10
2	6	F	68	loose thermal	2.04	10

LS refinement shell

Resolution: 2.59→2.654 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	68	-
R_work	0.297	1178	-
obs	-	-	51.07 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.707	0.0181	0.7675	5.6765	0.3729	5.332	0.2336	0.6703	-0.5309	-0.7311	-0.1423	0.1205	0.5082	-0.2587	-0.0913	-0.1494	0.0339	0.0899	-0.1721	-0.1272	-0.2644	13.926	-23.1635	-5.2954
2	6.0335	-1.2496	0.5878	5.557	-0.0727	5.2872	0.1307	-0.5385	-0.5504	0.2536	-0.0717	-0.1192	0.6775	0.1317	-0.0591	-0.3639	-0.0535	0.0323	-0.2688	-0.0015	-0.3231	10.4642	-21.592	16.1713
3	6.8159	0.2986	0.288	5.7351	0.8541	5.5417	0.0399	-0.0741	0.7448	-0.4036	-0.2495	1.0793	-0.5796	-1.1399	0.2096	-0.2533	0.1569	-0.0203	-0.0463	-0.0861	-0.1077	-8.6931	1.5644	14.416
4	6.2931	-0.4441	-0.0229	5.8145	1.3278	4.9626	0.1806	-0.7518	1.0709	0.0518	-0.0444	-0.0095	-0.6405	-0.1163	-0.1362	-0.0489	0.1416	0.0978	-0.2547	-0.0832	-0.011	6.88	16.9724	16.1894
5	4.9871	0.176	0.0838	3.2183	-0.6055	6.8923	-0.209	1.0173	0.6096	-0.911	0.1903	0.0622	-0.7123	0.0069	0.0188	0.4129	-0.0519	0.1558	-0.1537	0.1913	-0.0031	16.1306	14.7037	-12.04
6	6.0419	0.4871	0.8329	5.0659	-0.3148	5.1175	-0.1425	0.6252	0.3799	-0.7615	0.0837	-1.022	-0.3529	0.6062	0.0589	0.0292	-0.0345	0.344	-0.1888	0.0086	-0.0546	32.0901	0.0007	-7.5953

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 144	1 - 144
2	X-RAY DIFFRACTION	2	B	B	1 - 145	1 - 145
3	X-RAY DIFFRACTION	3	C	C	1 - 145	1 - 145
4	X-RAY DIFFRACTION	4	D	D	1 - 144	1 - 144
5	X-RAY DIFFRACTION	5	E	E	1 - 145	1 - 145
6	X-RAY DIFFRACTION	6	F	F	1 - 144	1 - 144

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