PDB-4i52: scMenB im complex with 1-hydroxy-2-naphthoyl-CoA

ID or keywords:

Entry

Database: PDB / ID: 4i52

Title

scMenB im complex with 1-hydroxy-2-naphthoyl-CoA

Components

Naphthoate synthase

Keywords

LYASE / crotonase / 1 / 4-dihydroxy-2-naphthoyl coenzyme A synthase

Function / homology

Function and homology information

1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / cytosol
Similarity search - Function

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Song, H.G. / Sun, Y.R. / Li, J. / Li, Y. / Jiang, M. / Zhou, J.H. / Guo, Z.H.

Citation

Journal: Plos One / Year: 2013
Title: Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily
Authors: Sun, Y. / Song, H. / Li, J. / Li, Y. / Jiang, M. / Zhou, J. / Guo, Z.

History

Deposition	Nov 28, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2013	Group: Database references
Revision 1.2	Nov 8, 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_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_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	4i52.cif.gz	493.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4i52.ent.gz	404 KB	Display	PDB format
PDBx/mmJSON format	4i52.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4i52_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	4i52_full_validation.pdf.gz	2.3 MB	Display
Data in XML	4i52_validation.xml.gz	99.6 KB	Display
Data in CIF	4i52_validation.cif.gz	126.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/4i52 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/4i52	HTTPS FTP

-
Related structure data

Related structure data	4i42C 4i4zC 4emlS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3h02-2 6dzs-2 2iex-d 3h02-3 3jbd-d 2dwp-1 6ha3-1 5165 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

4i42C

4i4zC

4emlS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Naphthoate synthase

B: Naphthoate synthase

C: Naphthoate synthase

D: Naphthoate synthase

E: Naphthoate synthase

F: Naphthoate synthase

G: Naphthoate synthase

H: Naphthoate synthase

I: Naphthoate synthase

hetero molecules

282 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Naphthoate synthase

C: Naphthoate synthase

D: Naphthoate synthase

hetero molecules

defined by author&software
93.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Naphthoate synthase

E: Naphthoate synthase

F: Naphthoate synthase

hetero molecules

defined by author&software
93.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Naphthoate synthase

H: Naphthoate synthase

I: Naphthoate synthase

hetero molecules

defined by author&software
93.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.843, 138.843, 221.217
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	D-462- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	PRO	PRO	A	A	1 - 275	1 - 275
2	1	MET	MET	PRO	PRO	B	B	1 - 275	1 - 275
1	2	ASP	ASP	LEU	LEU	A	A	2 - 274	2 - 274
2	2	ASP	ASP	LEU	LEU	C	C	2 - 274	2 - 274
1	3	MET	MET	PRO	PRO	A	A	1 - 275	1 - 275
2	3	MET	MET	PRO	PRO	D	D	1 - 275	1 - 275
1	4	ASP	ASP	LEU	LEU	A	A	2 - 274	2 - 274
2	4	ASP	ASP	LEU	LEU	E	E	2 - 274	2 - 274
1	5	ASP	ASP	LEU	LEU	A	A	2 - 274	2 - 274
2	5	ASP	ASP	LEU	LEU	F	F	2 - 274	2 - 274
1	6	MET	MET	PRO	PRO	A	A	1 - 275	1 - 275
2	6	MET	MET	PRO	PRO	G	G	1 - 275	1 - 275
1	7	MET	MET	PRO	PRO	A	A	1 - 275	1 - 275
2	7	MET	MET	PRO	PRO	H	H	1 - 275	1 - 275
1	8	MET	MET	PRO	PRO	A	A	1 - 275	1 - 275
2	8	MET	MET	PRO	PRO	I	I	1 - 275	1 - 275
1	9	ASP	ASP	LEU	LEU	B	B	2 - 274	2 - 274
2	9	ASP	ASP	LEU	LEU	C	C	2 - 274	2 - 274
1	10	MET	MET	PRO	PRO	B	B	1 - 275	1 - 275
2	10	MET	MET	PRO	PRO	D	D	1 - 275	1 - 275
1	11	ASP	ASP	LEU	LEU	B	B	2 - 274	2 - 274
2	11	ASP	ASP	LEU	LEU	E	E	2 - 274	2 - 274
1	12	ASP	ASP	LEU	LEU	B	B	2 - 274	2 - 274
2	12	ASP	ASP	LEU	LEU	F	F	2 - 274	2 - 274
1	13	MET	MET	PRO	PRO	B	B	1 - 275	1 - 275
2	13	MET	MET	PRO	PRO	G	G	1 - 275	1 - 275
1	14	MET	MET	PRO	PRO	B	B	1 - 275	1 - 275
2	14	MET	MET	PRO	PRO	H	H	1 - 275	1 - 275
1	15	MET	MET	PRO	PRO	B	B	1 - 275	1 - 275
2	15	MET	MET	PRO	PRO	I	I	1 - 275	1 - 275
1	16	ASP	ASP	LEU	LEU	C	C	2 - 274	2 - 274
2	16	ASP	ASP	LEU	LEU	D	D	2 - 274	2 - 274
1	17	ASP	ASP	PRO	PRO	C	C	2 - 275	2 - 275
2	17	ASP	ASP	PRO	PRO	E	E	2 - 275	2 - 275
1	18	ASP	ASP	PRO	PRO	C	C	2 - 275	2 - 275
2	18	ASP	ASP	PRO	PRO	F	F	2 - 275	2 - 275
1	19	ASP	ASP	LEU	LEU	C	C	2 - 274	2 - 274
2	19	ASP	ASP	LEU	LEU	G	G	2 - 274	2 - 274
1	20	ASP	ASP	LEU	LEU	C	C	2 - 274	2 - 274
2	20	ASP	ASP	LEU	LEU	H	H	2 - 274	2 - 274
1	21	ASP	ASP	LEU	LEU	C	C	2 - 274	2 - 274
2	21	ASP	ASP	LEU	LEU	I	I	2 - 274	2 - 274
1	22	ASP	ASP	LEU	LEU	D	D	2 - 274	2 - 274
2	22	ASP	ASP	LEU	LEU	E	E	2 - 274	2 - 274
1	23	ASP	ASP	LEU	LEU	D	D	2 - 274	2 - 274
2	23	ASP	ASP	LEU	LEU	F	F	2 - 274	2 - 274
1	24	MET	MET	PRO	PRO	D	D	1 - 275	1 - 275
2	24	MET	MET	PRO	PRO	G	G	1 - 275	1 - 275
1	25	MET	MET	PRO	PRO	D	D	1 - 275	1 - 275
2	25	MET	MET	PRO	PRO	H	H	1 - 275	1 - 275
1	26	MET	MET	PRO	PRO	D	D	1 - 275	1 - 275
2	26	MET	MET	PRO	PRO	I	I	1 - 275	1 - 275
1	27	ASP	ASP	PRO	PRO	E	E	2 - 275	2 - 275
2	27	ASP	ASP	PRO	PRO	F	F	2 - 275	2 - 275
1	28	ASP	ASP	LEU	LEU	E	E	2 - 274	2 - 274
2	28	ASP	ASP	LEU	LEU	G	G	2 - 274	2 - 274
1	29	ASP	ASP	LEU	LEU	E	E	2 - 274	2 - 274
2	29	ASP	ASP	LEU	LEU	H	H	2 - 274	2 - 274
1	30	ASP	ASP	LEU	LEU	E	E	2 - 274	2 - 274
2	30	ASP	ASP	LEU	LEU	I	I	2 - 274	2 - 274
1	31	ASP	ASP	LEU	LEU	F	F	2 - 274	2 - 274
2	31	ASP	ASP	LEU	LEU	G	G	2 - 274	2 - 274
1	32	ASP	ASP	LEU	LEU	F	F	2 - 274	2 - 274
2	32	ASP	ASP	LEU	LEU	H	H	2 - 274	2 - 274
1	33	ASP	ASP	LEU	LEU	F	F	2 - 274	2 - 274
2	33	ASP	ASP	LEU	LEU	I	I	2 - 274	2 - 274
1	34	MET	MET	PRO	PRO	G	G	1 - 275	1 - 275
2	34	MET	MET	PRO	PRO	H	H	1 - 275	1 - 275
1	35	MET	MET	PRO	PRO	G	G	1 - 275	1 - 275
2	35	MET	MET	PRO	PRO	I	I	1 - 275	1 - 275
1	36	MET	MET	PRO	PRO	H	H	1 - 275	1 - 275
2	36	MET	MET	PRO	PRO	I	I	1 - 275	1 - 275

NCS ensembles :

#1: Protein	Naphthoate synthase Mass: 30343.508 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa References: UniProt: P73495, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical	ChemComp-1HA / 1-hydroxy-2-naphthoyl-CoA Mass: 937.698 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃₂H₄₂N₇O₁₈P₃S
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 583 / 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: 45.43 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.15M ammonium acetate, 0.3M ammonium sulfate, 16% PEG3350, 100mM Bis-Tris buffer, 0.1M Proline(or 0.1M Taurine), pH 5.70, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2011
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.35→46.596 Å / Num. all: 97846 / Num. obs: 102666 / % possible obs: 99.73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.35→46.596 Å

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.7.0032	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4EML

4eml

Resolution: 2.35→46.596 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.905 / SU B: 8.258 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.582 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25556	5135	5 %	RANDOM
R_work	0.22884	-	-	-
obs	0.23016	97582	99.73 %	-
all	-	103005	-	-

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: 43.148 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.94 Å²	0.94 Å²	0 Å²
2-	-	0.94 Å²	0 Å²
3-	-	-	-3.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→46.596 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18830	0	558	583	19971

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	19834
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	18413
X-RAY DIFFRACTION	r_angle_refined_deg	1.297	1.992	26956
X-RAY DIFFRACTION	r_angle_other_deg	1.06	3	42207
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.973	5	2463
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.008	23.684	855
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.157	15	3056
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.435	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	2837
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	22635
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	4626

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15316	0.06
1	2	B	15316	0.06
2	1	A	15013	0.07
2	2	C	15013	0.07
3	1	A	15331	0.07
3	2	D	15331	0.07
4	1	A	15129	0.05
4	2	E	15129	0.05
5	1	A	15229	0.06
5	2	F	15229	0.06
6	1	A	15388	0.05
6	2	G	15388	0.05
7	1	A	15340	0.06
7	2	H	15340	0.06
8	1	A	15128	0.07
8	2	I	15128	0.07
9	1	B	15517	0.06
9	2	C	15517	0.06
10	1	B	15673	0.06
10	2	D	15673	0.06
11	1	B	15615	0.05
11	2	E	15615	0.05
12	1	B	15664	0.06
12	2	F	15664	0.06
13	1	B	15951	0.04
13	2	G	15951	0.04
14	1	B	15955	0.05
14	2	H	15955	0.05
15	1	B	15726	0.06
15	2	I	15726	0.06
16	1	C	15389	0.07
16	2	D	15389	0.07
17	1	C	15539	0.06
17	2	E	15539	0.06
18	1	C	15560	0.06
18	2	F	15560	0.06
19	1	C	15473	0.06
19	2	G	15473	0.06
20	1	C	15562	0.06
20	2	H	15562	0.06
21	1	C	15406	0.06
21	2	I	15406	0.06
22	1	D	15532	0.06
22	2	E	15532	0.06
23	1	D	15672	0.05
23	2	F	15672	0.05
24	1	D	15718	0.06
24	2	G	15718	0.06
25	1	D	15770	0.06
25	2	H	15770	0.06
26	1	D	15688	0.06
26	2	I	15688	0.06
27	1	E	15646	0.06
27	2	F	15646	0.06
28	1	E	15583	0.04
28	2	G	15583	0.04
29	1	E	15711	0.05
29	2	H	15711	0.05
30	1	E	15561	0.06
30	2	I	15561	0.06
31	1	F	15670	0.06
31	2	G	15670	0.06
32	1	F	15784	0.06
32	2	H	15784	0.06
33	1	F	15722	0.05
33	2	I	15722	0.05
34	1	G	15886	0.06
34	2	H	15886	0.06
35	1	G	15716	0.06
35	2	I	15716	0.06
36	1	H	15925	0.06
36	2	I	15925	0.06

LS refinement shell

Resolution: 2.35→2.412 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	346	-
R_work	0.269	7109	-
obs	-	97582	99.67 %

-
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

+
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