PDB-1q51: Crystal Structure of Mycobacterium tuberculosis MenB in Complex w...

ID or keywords:

Entry

Database: PDB / ID: 1q51

Title

Crystal Structure of Mycobacterium tuberculosis MenB in Complex with Acetoacetyl-Coenzyme A, a Key Enzyme in Vitamin K2 Biosynthesis

Components

menB

Keywords

LYASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Truglio, J.J. / Theis, K. / Feng, Y. / Gajda, R. / Machutta, C. / Tonge, P.J. / Kisker, C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis.
Authors: Truglio, J.J. / Theis, K. / Feng, Y. / Gajda, R. / Machutta, C. / Tonge, P.J. / Kisker, C.

History

Deposition	Aug 5, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Aug 16, 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.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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	1q51.cif.gz	646 KB	Display	PDBx/mmCIF format
PDB format	pdb1q51.ent.gz	539 KB	Display	PDB format
PDBx/mmJSON format	1q51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/1q51 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/1q51	HTTPS FTP

-
Related structure data

Related structure data	1q52C 1dubS 1dci 1ef8 1hnu 1nzy 1o8u S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4nek-d 4i42-1 1q52-2 6ojm-2 4zdc-1 4zdf-1 4jcs-1 4qij-1 1q52-1 6ojm-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: Rv0548c

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: menB

B: menB

C: menB

D: menB

E: menB

F: menB

G: menB

H: menB

I: menB

J: menB

K: menB

L: menB

hetero molecules

427 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: menB

B: menB

C: menB

D: menB

E: menB

F: menB

hetero molecules

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

2

G: menB

H: menB

I: menB

J: menB

K: menB

L: menB

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.401, 139.389, 142.041
Angle α, β, γ (deg.)	90.00, 97.31, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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	ASN	ASN	PHE	PHE	2	A	A	18 - 314	18 - 314
2	1	1	ASN	ASN	PHE	PHE	2	B	B	18 - 314	18 - 314
3	1	1	ASN	ASN	PHE	PHE	2	C	C	18 - 314	18 - 314
4	1	1	ASN	ASN	PHE	PHE	2	D	D	18 - 314	18 - 314
5	1	1	ASN	ASN	PHE	PHE	2	E	E	18 - 314	18 - 314
6	1	1	ASN	ASN	PHE	PHE	2	F	F	18 - 314	18 - 314
7	1	1	ASN	ASN	PHE	PHE	2	G	G	18 - 314	18 - 314
8	1	1	ASN	ASN	PHE	PHE	2	H	H	18 - 314	18 - 314
9	1	1	ASN	ASN	PHE	PHE	2	I	I	18 - 314	18 - 314
10	1	1	ASN	ASN	PHE	PHE	2	J	J	18 - 314	18 - 314
11	1	1	ASN	ASN	PHE	PHE	2	K	K	18 - 314	18 - 314
12	1	1	ASN	ASN	PHE	PHE	2	L	L	18 - 314	18 - 314
13	2	1	HOH	HOH	HOH	HOH	4	A	Y	502 - 524
14	2	1	HOH	HOH	HOH	HOH	4	B	Z	504 - 528
15	2	1	HOH	HOH	HOH	HOH	4	C - E	AA - CA	505 - 507
16	2	1	HOH	HOH	HOH	HOH	4	D - A	BA - Y	506 - 532
17	2	1	HOH	HOH	HOH	HOH	4	E - C	CA - AA	510 - 535
18	2	1	HOH	HOH	HOH	HOH	4	D - B	BA - Z	535 - 537
19	2	1	HOH	HOH	HOH	HOH	4	G	EA	509 - 530
20	2	1	HOH	HOH	HOH	HOH	4	G - H	EA - FA	531 - 533
21	2	1	HOH	HOH	HOH	HOH	4	G - I	EA - GA	534 - 541
22	2	1	HOH	HOH	HOH	HOH	4	K - G	IA - EA	534 - 542
23	2	1	HOH	HOH	HOH	HOH	4	K - I	IA - GA	501 - 515
24	2	1	HOH	HOH	HOH	HOH	4	L - H	JA - FA	518 - 542
1	1	2	CAA	CAA	CAA	CAA	1	A	M	501
2	1	2	CAA	CAA	CAA	CAA	1	B	N	502
3	1	2	CAA	CAA	CAA	CAA	1	C	O	503
4	1	2	CAA	CAA	CAA	CAA	1	D	P	504
5	1	2	CAA	CAA	CAA	CAA	1	E	Q	505
6	1	2	CAA	CAA	CAA	CAA	1	F	R	506
7	1	2	CAA	CAA	CAA	CAA	1	G	S	507
8	1	2	CAA	CAA	CAA	CAA	1	H	T	508
9	1	2	CAA	CAA	CAA	CAA	1	I	U	509
10	1	2	CAA	CAA	CAA	CAA	1	J	V	510
11	1	2	CAA	CAA	CAA	CAA	1	K	W	500
12	1	2	CAA	CAA	CAA	CAA	1	L	X	511

NCS ensembles :

ID
1
2

#1: Protein	menB Mass: 34731.938 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: menB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: O06414, UniProt: P9WNP5*PLUS, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical	ChemComp-CAA / ACETOACETYL-COENZYME A Mass: 851.607 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₅H₄₀N₇O₁₈P₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.13 Å³/Da / Density % sol: 42.22 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal grow

*PLUS

Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	0.5-2 %	dioxane	1	reservoir
2	1.2-1.3 M	ammonium sulfate	1	reservoir
3	0.1 M	MES	1	reservoir	pH6.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2002
Radiation	Monochromator: null / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 146353
Reflection	PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % possible obs: 99.7 % / Num. measured all: 503676 / R_merge(I) obs*: 0.116
Reflection shell	PLUS R_merge(I) obs: 0.551 / Mean I/σ(I) obs*: 2

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
CCP4		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DUB

1dub

Resolution: 2.3→50 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.917 / SU B: 7.855 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24106	7777	5 %	RANDOM
R_work	0.20171	-	-	-
all	0.20369	-	-	-
obs	0.20369	146353	99.62 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.919 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.24 Å²	0 Å²	0.1 Å²
2-	-	-1.59 Å²	0 Å²
3-	-	-	-2.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25697	0	648	422	26767

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	27017
X-RAY DIFFRACTION	r_angle_refined_deg	1.495	1.956	36712
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.394	5	3237
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	3827
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	21278
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	12903
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	1446
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.22	0.2	52
X-RAY DIFFRACTION	r_mcbond_it	0.639	1.5	16136
X-RAY DIFFRACTION	r_mcangle_it	1.231	2	25714
X-RAY DIFFRACTION	r_scbond_it	1.831	3	10881
X-RAY DIFFRACTION	r_scangle_it	2.895	4.5	10998

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	1084	tight positional	0.05	0.05
1	2	B	1084	tight positional	0.06	0.05
1	3	C	1084	tight positional	0.05	0.05
1	4	D	1084	tight positional	0.05	0.05
1	5	E	1084	tight positional	0.05	0.05
1	6	F	1084	tight positional	0.05	0.05
1	7	G	1084	tight positional	0.05	0.05
1	8	H	1084	tight positional	0.05	0.05
1	9	I	1084	tight positional	0.05	0.05
1	10	J	1084	tight positional	0.05	0.05
1	11	K	1084	tight positional	0.05	0.05
1	12	L	1084	tight positional	0.05	0.05
2	1	A	54	tight positional	0.02	0.05
2	2	B	54	tight positional	0.02	0.05
2	3	C	54	tight positional	0.03	0.05
2	4	D	54	tight positional	0.02	0.05
2	5	E	54	tight positional	0.03	0.05
2	6	F	54	tight positional	0.03	0.05
2	7	G	54	tight positional	0.03	0.05
2	8	H	54	tight positional	0.02	0.05
2	9	I	54	tight positional	0.02	0.05
2	10	J	54	tight positional	0.03	0.05
2	11	K	54	tight positional	0.03	0.05
2	12	L	54	tight positional	0.02	0.05
1	1	A	1077	medium positional	0.38	0.5
1	2	B	1077	medium positional	0.47	0.5
1	3	C	1077	medium positional	0.34	0.5
1	4	D	1077	medium positional	0.34	0.5
1	5	E	1077	medium positional	0.3	0.5
1	6	F	1077	medium positional	0.29	0.5
1	7	G	1077	medium positional	0.36	0.5
1	8	H	1077	medium positional	0.3	0.5
1	9	I	1077	medium positional	0.44	0.5
1	10	J	1077	medium positional	0.35	0.5
1	11	K	1077	medium positional	0.38	0.5
1	12	L	1077	medium positional	0.42	0.5
1	1	A	1084	tight thermal	0.17	0.5
1	2	B	1084	tight thermal	0.14	0.5
1	3	C	1084	tight thermal	0.13	0.5
1	4	D	1084	tight thermal	0.16	0.5
1	5	E	1084	tight thermal	0.12	0.5
1	6	F	1084	tight thermal	0.12	0.5
1	7	G	1084	tight thermal	0.13	0.5
1	8	H	1084	tight thermal	0.13	0.5
1	9	I	1084	tight thermal	0.16	0.5
1	10	J	1084	tight thermal	0.12	0.5
1	11	K	1084	tight thermal	0.12	0.5
1	12	L	1084	tight thermal	0.15	0.5
2	1	A	54	tight thermal	0.11	0.5
2	2	B	54	tight thermal	0.08	0.5
2	3	C	54	tight thermal	0.07	0.5
2	4	D	54	tight thermal	0.07	0.5
2	5	E	54	tight thermal	0.08	0.5
2	6	F	54	tight thermal	0.08	0.5
2	7	G	54	tight thermal	0.07	0.5
2	8	H	54	tight thermal	0.1	0.5
2	9	I	54	tight thermal	0.08	0.5
2	10	J	54	tight thermal	0.07	0.5
2	11	K	54	tight thermal	0.08	0.5
2	12	L	54	tight thermal	0.07	0.5
1	1	A	1077	medium thermal	1.23	2
1	2	B	1077	medium thermal	1.09	2
1	3	C	1077	medium thermal	0.98	2
1	4	D	1077	medium thermal	1.06	2
1	5	E	1077	medium thermal	0.94	2
1	6	F	1077	medium thermal	0.91	2
1	7	G	1077	medium thermal	0.98	2
1	8	H	1077	medium thermal	0.97	2
1	9	I	1077	medium thermal	1.06	2
1	10	J	1077	medium thermal	0.86	2
1	11	K	1077	medium thermal	1.04	2
1	12	L	1077	medium thermal	1.06	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.318	615
R_work	0.275	10759

Refinement

*PLUS

Lowest resolution: 50 Å / R_factor R_free: 0.243 / R_factor R_work: 0.203

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.015
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.5

-
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