PDB-3az9: Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Pla...

ID or keywords:

Entry

Database: PDB / ID: 3az9

Title

Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum in complex with NAS91

Components

Beta-hydroxyacyl-ACP dehydratase

Keywords

LYASE/INHIBITOR / hot dog fold / FabZ / beta-hydroxyacyl acyl carrier protein dehydratase / Lyase / acyl carrier protein / LYASE-INHIBITOR complex

Function / homology

Function and homology information

3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / lipid A biosynthetic process / fatty acid biosynthetic process / membrane / cytoplasm
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Maity, K. / Venkata, B.S. / Kapoor, N. / Surolia, N. / Surolia, A. / Suguna, K.

Citation

Journal: J.Struct.Biol. / Year: 2011
Title: Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum
Authors: Maity, K. / Venkata, B.S. / Kapoor, N. / Surolia, N. / Surolia, A. / Suguna, K.

History

Deposition	May 21, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3az9.cif.gz	658.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3az9.ent.gz	542.6 KB	Display	PDB format
PDBx/mmJSON format	3az9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3az9_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	3az9_full_validation.pdf.gz	3 MB	Display
Data in XML	3az9_validation.xml.gz	134 KB	Display
Data in CIF	3az9_validation.cif.gz	172.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/3az9 ftp://data.pdbj.org/pub/pdb/validation_reports/az/3az9	HTTPS FTP

-
Related structure data

Related structure data	3az8C 3azaC 3azbC 1z6bS 1zhg S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3aza-1 3az8-1 3aza-3 3aza-4 3azb-4 3aza-2 3az8-3 3azb-2 3az8-4 3azb-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

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

Deposited unit

A: Beta-hydroxyacyl-ACP dehydratase

B: Beta-hydroxyacyl-ACP dehydratase

C: Beta-hydroxyacyl-ACP dehydratase

D: Beta-hydroxyacyl-ACP dehydratase

E: Beta-hydroxyacyl-ACP dehydratase

F: Beta-hydroxyacyl-ACP dehydratase

G: Beta-hydroxyacyl-ACP dehydratase

H: Beta-hydroxyacyl-ACP dehydratase

I: Beta-hydroxyacyl-ACP dehydratase

J: Beta-hydroxyacyl-ACP dehydratase

K: Beta-hydroxyacyl-ACP dehydratase

L: Beta-hydroxyacyl-ACP dehydratase

M: Beta-hydroxyacyl-ACP dehydratase

N: Beta-hydroxyacyl-ACP dehydratase

O: Beta-hydroxyacyl-ACP dehydratase

P: Beta-hydroxyacyl-ACP dehydratase

Q: Beta-hydroxyacyl-ACP dehydratase

R: Beta-hydroxyacyl-ACP dehydratase

S: Beta-hydroxyacyl-ACP dehydratase

T: Beta-hydroxyacyl-ACP dehydratase

U: Beta-hydroxyacyl-ACP dehydratase

V: Beta-hydroxyacyl-ACP dehydratase

W: Beta-hydroxyacyl-ACP dehydratase

X: Beta-hydroxyacyl-ACP dehydratase

hetero molecules

413 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-hydroxyacyl-ACP dehydratase

B: Beta-hydroxyacyl-ACP dehydratase

C: Beta-hydroxyacyl-ACP dehydratase

D: Beta-hydroxyacyl-ACP dehydratase

E: Beta-hydroxyacyl-ACP dehydratase

F: Beta-hydroxyacyl-ACP dehydratase

hetero molecules

defined by author&software
104 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Beta-hydroxyacyl-ACP dehydratase

H: Beta-hydroxyacyl-ACP dehydratase

I: Beta-hydroxyacyl-ACP dehydratase

J: Beta-hydroxyacyl-ACP dehydratase

K: Beta-hydroxyacyl-ACP dehydratase

L: Beta-hydroxyacyl-ACP dehydratase

hetero molecules

defined by author&software
103 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: Beta-hydroxyacyl-ACP dehydratase

N: Beta-hydroxyacyl-ACP dehydratase

O: Beta-hydroxyacyl-ACP dehydratase

P: Beta-hydroxyacyl-ACP dehydratase

Q: Beta-hydroxyacyl-ACP dehydratase

R: Beta-hydroxyacyl-ACP dehydratase

hetero molecules

defined by author&software
104 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

S: Beta-hydroxyacyl-ACP dehydratase

T: Beta-hydroxyacyl-ACP dehydratase

U: Beta-hydroxyacyl-ACP dehydratase

V: Beta-hydroxyacyl-ACP dehydratase

W: Beta-hydroxyacyl-ACP dehydratase

X: Beta-hydroxyacyl-ACP dehydratase

hetero molecules

defined by author&software
103 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	216.680, 216.680, 156.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	80
Space group name H-M	I4₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 89 - 227 / Label seq-ID: 13 - 151

#1: Protein	... Beta-hydroxyacyl-ACP dehydratase / beta-hydroxyacyl-acyl carrier protein dehydratase / Fatty acid synthesis protein Mass: 17038.904 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: fabz / Plasmid: PET-28a(+)(NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q965D7, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-K91 / 4-chloro-2-[(5-chloroquinolin-8-yl)oxy]phenol Mass: 306.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₉Cl₂NO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.32 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20-25% PEG 8000, 0.1M MES, 0.1-0.3M KH2PO4, 15-20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM14 / Wavelength: 0.97 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.512
1	1	-H, K, -L	2	0.488

Reflection

Resolution: 2.75→54.15 Å / Num. obs: 93862 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / B_iso Wilson estimate: 58.68 Å² / R_sym value: 0.162 / Net I/σ(I): 7.7

Reflection shell

Resolution: 2.75→2.9 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 13657 / R_sym value: 0.576 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Z6B

1z6b

Resolution: 2.75→51.58 Å / Cor.coef. F_o:F_c: 0.886 / Cor.coef. F_o:F_c free: 0.834 / SU B: 20.63 / SU ML: 0.383 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28188	4784	5.1 %	RANDOM
R_work	0.23364	-	-	-
obs	0.23611	88993	99.75 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 40.458 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.72 Å²	0 Å²	0 Å²
2-	-	8.72 Å²	0 Å²
3-	-	-	-17.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→51.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26735	0	249	430	27414

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	27513
X-RAY DIFFRACTION	r_angle_refined_deg	1.405	1.988	37226
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.168	5	3441
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.626	25.852	1039
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.303	15	4933
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.856	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	4323
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	20005
X-RAY DIFFRACTION	r_mcbond_it	0.479	1.5	17240
X-RAY DIFFRACTION	r_mcangle_it	0.846	2	27960
X-RAY DIFFRACTION	r_scbond_it	0.918	3	10273
X-RAY DIFFRACTION	r_scangle_it	1.519	4.5	9266

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	536	tight positional	0.08	0.05
2	B	536	tight positional	0.09	0.05
3	C	536	tight positional	0.09	0.05
4	D	536	tight positional	0.11	0.05
5	E	536	tight positional	0.08	0.05
6	F	536	tight positional	0.08	0.05
7	G	536	tight positional	0.08	0.05
8	H	536	tight positional	0.08	0.05
9	I	536	tight positional	0.09	0.05
10	J	536	tight positional	0.08	0.05
11	K	536	tight positional	0.08	0.05
12	L	536	tight positional	0.09	0.05
13	M	536	tight positional	0.07	0.05
14	N	536	tight positional	0.08	0.05
15	O	536	tight positional	0.08	0.05
16	P	536	tight positional	0.08	0.05
17	Q	536	tight positional	0.09	0.05
18	R	536	tight positional	0.08	0.05
19	S	536	tight positional	0.09	0.05
20	T	536	tight positional	0.09	0.05
21	U	536	tight positional	0.09	0.05
22	V	536	tight positional	0.08	0.05
23	W	536	tight positional	0.09	0.05
24	X	536	tight positional	0.09	0.05
1	A	491	loose positional	0.18	5
2	B	491	loose positional	0.11	5
3	C	491	loose positional	0.12	5
4	D	491	loose positional	0.16	5
5	E	491	loose positional	0.1	5
6	F	491	loose positional	0.12	5
7	G	491	loose positional	0.16	5
8	H	491	loose positional	0.13	5
9	I	491	loose positional	0.16	5
10	J	491	loose positional	0.11	5
11	K	491	loose positional	0.16	5
12	L	491	loose positional	0.12	5
13	M	491	loose positional	0.13	5
14	N	491	loose positional	0.13	5
15	O	491	loose positional	0.13	5
16	P	491	loose positional	0.13	5
17	Q	491	loose positional	0.14	5
18	R	491	loose positional	0.13	5
19	S	491	loose positional	0.11	5
20	T	491	loose positional	0.13	5
21	U	491	loose positional	0.17	5
22	V	491	loose positional	0.13	5
23	W	491	loose positional	0.19	5
24	X	491	loose positional	0.14	5
1	A	536	tight thermal	0.18	0.5
2	B	536	tight thermal	0.21	0.5
3	C	536	tight thermal	0.37	0.5
4	D	536	tight thermal	0.27	0.5
5	E	536	tight thermal	0.24	0.5
6	F	536	tight thermal	0.25	0.5
7	G	536	tight thermal	0.19	0.5
8	H	536	tight thermal	0.19	0.5
9	I	536	tight thermal	0.28	0.5
10	J	536	tight thermal	0.17	0.5
11	K	536	tight thermal	0.2	0.5
12	L	536	tight thermal	0.2	0.5
13	M	536	tight thermal	0.16	0.5
14	N	536	tight thermal	0.19	0.5
15	O	536	tight thermal	0.24	0.5
16	P	536	tight thermal	0.3	0.5
17	Q	536	tight thermal	0.19	0.5
18	R	536	tight thermal	0.37	0.5
19	S	536	tight thermal	0.26	0.5
20	T	536	tight thermal	0.25	0.5
21	U	536	tight thermal	0.24	0.5
22	V	536	tight thermal	0.27	0.5
23	W	536	tight thermal	0.25	0.5
24	X	536	tight thermal	0.28	0.5
1	A	491	loose thermal	0.22	10
2	B	491	loose thermal	0.21	10
3	C	491	loose thermal	0.46	10
4	D	491	loose thermal	0.59	10
5	E	491	loose thermal	0.26	10
6	F	491	loose thermal	0.26	10
7	G	491	loose thermal	0.22	10
8	H	491	loose thermal	0.24	10
9	I	491	loose thermal	0.35	10
10	J	491	loose thermal	0.22	10
11	K	491	loose thermal	0.27	10
12	L	491	loose thermal	0.22	10
13	M	491	loose thermal	0.31	10
14	N	491	loose thermal	0.24	10
15	O	491	loose thermal	0.41	10
16	P	491	loose thermal	0.34	10
17	Q	491	loose thermal	0.28	10
18	R	491	loose thermal	0.44	10
19	S	491	loose thermal	0.26	10
20	T	491	loose thermal	0.31	10
21	U	491	loose thermal	0.33	10
22	V	491	loose thermal	0.32	10
23	W	491	loose thermal	0.32	10
24	X	491	loose thermal	0.32	10

LS refinement shell

Resolution: 2.749→2.82 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.33	360	-
R_work	0.246	6424	-
obs	-	-	97.74 %

-
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://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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi