PDB-2gek: Crystal Structure of phosphatidylinositol mannosyltransferase (Pi...

ID or keywords:

Entry

Database: PDB / ID: 2gek

Title

Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP

Components

PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA)

Keywords

TRANSFERASE / GT4 GLYCOSYLTRANSFERASE / MANNOSYLTRANSFERASE / ROSSMANN FOLD / BINARY COMPLEX

Function / homology

Function and homology information

GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity / phosphatidyl-myo-inositol alpha-mannosyltransferase / phosphatidylinositol alpha-mannosyltransferase activity / glycolipid biosynthetic process / phosphatidylinositol metabolic process / phospholipid biosynthetic process / plasma membrane
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Guerin, M.E. / Buschiazzo, A. / Kordulakova, J. / Jackson, M. / Alzari, P.M.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Molecular recognition and interfacial catalysis by the essential phosphatidylinositol mannosyltransferase PimA from mycobacteria.
Authors: Guerin, M.E. / Kordulakova, J. / Schaeffer, F. / Svetlikova, Z. / Buschiazzo, A. / Giganti, D. / Gicquel, B. / Mikusova, K. / Jackson, M. / Alzari, P.M.

History

Deposition	Mar 20, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE NO SUITABLE SEQUENCE DATABSE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS FILE.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gek.cif.gz	85.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2gek.ent.gz	61 KB	Display	PDB format
PDBx/mmJSON format	2gek.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ge/2gek ftp://data.pdbj.org/pub/pdb/validation_reports/ge/2gek	HTTPS FTP

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Related structure data

Related structure data	2gejC C: citing same article (ref.)
Similar structure data	2gej-d 3zho-d 6zot-d 6ylr-d 3h5l-2 2fa1-d 1wwz-d 3jz3-d 2ocx-d 6ha0-d 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

Deposited unit

A: PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA)

hetero molecules

43.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	37.176, 72.425, 138.230
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA) Mass: 43440.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: PIMA / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: A0QWG6
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.42 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 MG/ML PIMA, 1 mM GDP, 10-18% PEG 8000, 200 mM CALCIUM ACETATE, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID14-1	1	0.934
SYNCHROTRON	SLS	X06SA	2	0.979106, 0.979261, 0.97181

Detector

Type	ID	Detector	Date
ADSC QUANTUM 4	1	CCD	Jun 13, 2004
MARRESEARCH	2	CCD	Jul 31, 2005

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	DIAMOND (111), GE (220)	SINGLE WAVELENGTH	M	x-ray	1
2	LN2 COOLED FIXED-EXIT Si(111)	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.934	1
2	0.979106	1
3	0.979261	1
4	0.97181	1

Reflection

% possible obs: 100

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	Num. obs
14.2	1	5.3	78479	0.115	0.115	3.4	72.932	5527
6.6	2	7.3	52690	0.08	0.08	3	72.169	8000
6.5	3	7.4	52298	0.084	0.084	3	72.169	8023

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
10.75	73.02	222	99.8	1	0.064	0.064	11.2
7.6	10.75	345	100	1	0.063	0.063	13.2
6.21	7.6	422	100	1	0.094	0.094	13.7
5.38	6.21	500	100	1	0.118	0.118	14.1
4.81	5.38	565	100	1	0.108	0.108	14.3
4.39	4.81	623	100	1	0.107	0.107	14.4
4.06	4.39	639	100	1	0.116	0.116	14.6
3.8	4.06	700	100	1	0.143	0.143	14.6
3.58	3.8	745	100	1	0.181	0.181	14.6
3.4	3.58	766	100	1	0.238	0.238	14.6
9.49	72.17	307	99.2	2	0.035	0.035	5.4
6.71	9.49	500	99.9	2	0.042	0.042	6.2
5.48	6.71	619	100	2	0.083	0.083	6.4
4.74	5.48	716	100	2	0.072	0.072	6.5
4.24	4.74	794	100	2	0.068	0.068	6.6
3.87	4.24	903	100	2	0.074	0.074	6.6
3.59	3.87	945	100	2	0.095	0.095	6.7
3.35	3.59	1005	100	2	0.126	0.126	6.8
3.16	3.35	1078	100	2	0.176	0.176	6.8
3	3.16	1133	100	2	0.256	0.256	6.7
9.49	72.17	310	99.8	3	0.033	0.033	5.3
6.71	9.49	503	100	3	0.04	0.04	6.1
5.48	6.71	619	100	3	0.082	0.082	6.4
4.74	5.48	718	100	3	0.072	0.072	6.5
4.24	4.74	796	100	3	0.065	0.065	6.6
3.87	4.24	904	100	3	0.074	0.074	6.6
3.59	3.87	946	100	3	0.102	0.102	6.7
3.35	3.59	1011	100	3	0.146	0.146	6.7
3.16	3.35	1083	100	3	0.222	0.222	6.6
3	3.16	1133	100	3	0.34	0.34	6.6

Reflection

Resolution: 2.4→37.165 Å / Num. all: 15229 / Num. obs: 15229 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / R_merge(I) obs: 0.058 / R_sym value: 0.058 / Net I/σ(I): 9

Reflection shell

Resolution: 2.4→2.53 Å / % possible obs: 100 % / Redundancy: 3.4 % / R_merge(I) obs: 0.313 / Mean I/σ(I) obs: 2.4 / Num. measured all: 7327 / Num. unique obs: 2175 / R_sym value: 0.313 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 3.5 Å / D res low: 69.96 Å / FOM acentric: 0.727 / FOM centric: 0.603 / Reflection acentric: 4015 / Reflection centric: 1053

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	3.5	69.96	0	0	4015	1053
ISO_2	3.5	69.96	1.298	1.05	4015	1042
ISO_3	3.5	69.96	1.86	1.386	4015	1036
ANO_1	3.5	69.96	2.092	0	4015	0
ANO_2	3.5	69.96	0.978	0	4014	0
ANO_3	3.5	69.96	0.84	0	4013	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	12.43-69.96	0	0	59	73
ISO_1	8.86-12.43	0	0	136	71
ISO_1	7.26-8.86	0	0	188	80
ISO_1	6.29-7.26	0	0	230	79
ISO_1	5.63-6.29	0	0	273	87
ISO_1	5.14-5.63	0	0	295	87
ISO_1	4.76-5.14	0	0	326	81
ISO_1	4.46-4.76	0	0	351	84
ISO_1	4.2-4.46	0	0	387	71
ISO_1	3.99-4.2	0	0	410	86
ISO_1	3.8-3.99	0	0	425	84
ISO_1	3.64-3.8	0	0	459	85
ISO_1	3.5-3.64	0	0	476	85
ANO_1	12.43-69.96	5.038	0	59	0
ANO_1	8.86-12.43	3.978	0	136	0
ANO_1	7.26-8.86	4.137	0	188	0
ANO_1	6.29-7.26	3.934	0	230	0
ANO_1	5.63-6.29	3.234	0	273	0
ANO_1	5.14-5.63	2.683	0	295	0
ANO_1	4.76-5.14	2.352	0	326	0
ANO_1	4.46-4.76	2.039	0	351	0
ANO_1	4.2-4.46	1.774	0	387	0
ANO_1	3.99-4.2	1.479	0	410	0
ANO_1	3.8-3.99	1.349	0	425	0
ANO_1	3.64-3.8	1.124	0	459	0
ANO_1	3.5-3.64	0.982	0	476	0
ISO_2	12.43-69.96	3.14	1.981	59	71
ISO_2	8.86-12.43	2.081	1.722	136	71
ISO_2	7.26-8.86	2.299	1.606	188	80
ISO_2	6.29-7.26	2.509	1.813	230	79
ISO_2	5.63-6.29	2.07	1	273	84
ISO_2	5.14-5.63	1.674	1.138	295	86
ISO_2	4.76-5.14	1.356	0.923	326	81
ISO_2	4.46-4.76	1.18	0.908	351	84
ISO_2	4.2-4.46	0.989	0.681	387	71
ISO_2	3.99-4.2	0.95	0.52	410	86
ISO_2	3.8-3.99	0.781	0.501	425	83
ISO_2	3.64-3.8	0.753	0.465	459	83
ISO_2	3.5-3.64	0.702	0.442	476	83
ANO_2	12.43-69.96	2.757	0	59	0
ANO_2	8.86-12.43	1.824	0	136	0
ANO_2	7.26-8.86	2.301	0	188	0
ANO_2	6.29-7.26	1.763	0	230	0
ANO_2	5.63-6.29	1.3	0	273	0
ANO_2	5.14-5.63	1.202	0	295	0
ANO_2	4.76-5.14	0.962	0	326	0
ANO_2	4.46-4.76	0.915	0	350	0
ANO_2	4.2-4.46	0.805	0	387	0
ANO_2	3.99-4.2	0.682	0	410	0
ANO_2	3.8-3.99	0.684	0	425	0
ANO_2	3.64-3.8	0.536	0	459	0
ANO_2	3.5-3.64	0.488	0	476	0
ISO_3	12.43-69.96	4.665	3.37	59	73
ISO_3	8.86-12.43	3.299	2.748	136	71
ISO_3	7.26-8.86	3.698	2.212	188	80
ISO_3	6.29-7.26	3.587	2.036	230	77
ISO_3	5.63-6.29	2.97	1.379	273	84
ISO_3	5.14-5.63	2.599	1.221	295	84
ISO_3	4.76-5.14	2.099	1.147	326	81
ISO_3	4.46-4.76	1.846	1.117	351	81
ISO_3	4.2-4.46	1.607	0.98	387	71
ISO_3	3.99-4.2	1.379	0.787	410	85
ISO_3	3.8-3.99	1.164	0.715	425	83
ISO_3	3.64-3.8	0.948	0.51	459	82
ISO_3	3.5-3.64	0.873	0.566	476	84
ANO_3	12.43-69.96	1.421	0	59	0
ANO_3	8.86-12.43	1.371	0	136	0
ANO_3	7.26-8.86	1.503	0	188	0
ANO_3	6.29-7.26	1.395	0	230	0
ANO_3	5.63-6.29	1.199	0	273	0
ANO_3	5.14-5.63	0.972	0	295	0
ANO_3	4.76-5.14	0.924	0	326	0
ANO_3	4.46-4.76	0.799	0	351	0
ANO_3	4.2-4.46	0.862	0	387	0
ANO_3	3.99-4.2	0.644	0	410	0
ANO_3	3.8-3.99	0.578	0	424	0
ANO_3	3.64-3.8	0.44	0	459	0
ANO_3	3.5-3.64	0.407	0	475	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	1.542	43.222	12.241	SE	37.51	1.36
2	-4.077	46.418	44.688	SE	86.81	1.46
3	7.183	32.694	33.097	SE	61.22	1.01
4	5.662	36.769	3.537	SE	107.74	1.53
5	-1.461	36.551	45.389	SE	116.71	1.32
6	7.408	42.994	35.091	SE	0	1.68
7	7.723	35.661	6.759	SE	60.31	0.85
8	21.073	40.229	10.654	SE	48.12	0.67
9	6.926	58.135	55.191	SE	181.25	1.41

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
12.43-69.96	0.923	0.832	59	73
8.86-12.43	0.897	0.781	136	71
7.26-8.86	0.917	0.766	188	80
6.29-7.26	0.914	0.814	230	79
5.63-6.29	0.893	0.658	273	87
5.14-5.63	0.852	0.641	295	87
4.76-5.14	0.803	0.579	326	81
4.46-4.76	0.789	0.606	351	84
4.2-4.46	0.743	0.633	387	71
3.99-4.2	0.685	0.466	410	86
3.8-3.99	0.603	0.44	425	84
3.64-3.8	0.568	0.346	459	85
3.5-3.64	0.505	0.369	476	85

Phasing MR

R_factor: 0.397 / Cor.coef. F_o:F_c: 0.582 / Cor.coef. Io to Ic: 0.536

	Highest resolution	Lowest resolution
Rotation	4 Å	15 Å
Translation	4 Å	15 Å

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Processing

Software

Name	Version	Classification
SCALA		data scaling
AMoRE		phasing
SHARP		phasing
SOLOMON		phasing
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.4→29.827 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.908 / SU B: 18.435 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	1090	7.2 %	RANDOM
R_work	0.191	-	-	-
all	0.196	15202	-	-
obs	0.196	15202	99.47 %	-

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: 36.819 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.21 Å²	0 Å²	0 Å²
2-	-	-0.94 Å²	0 Å²
3-	-	-	-0.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→29.827 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2656	0	28	49	2733

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2739
X-RAY DIFFRACTION	r_angle_refined_deg	1.857	1.974	3736
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.694	5	359
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.634	22.897	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.446	15	404
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.226	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	432
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2078
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	1165
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	1810
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	106
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.241	0.2	25
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.153	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.863	1.5	1838
X-RAY DIFFRACTION	r_mcangle_it	1.279	2	2841
X-RAY DIFFRACTION	r_scbond_it	2.263	3	1033
X-RAY DIFFRACTION	r_scangle_it	3.426	4.5	895

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.41	68	-
R_work	0.235	1040	-
obs	-	1108	99.82 %

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	3.5829	-1.5446	0.8505	4.6285	-0.684	3.8028	-0.0057	0.1579	-0.1862	-0.0287	0.0985	0.0543	-0.0228	0.0133	-0.0929	-0.3619	-0.0085	-0.0286	-0.1529	-0.0048	-0.2163	-5.048	40.022	11.575
2	3.6694	-0.4879	0.1392	3.4664	0.8713	7.8955	-0.1633	-0.3124	0.1465	1.0339	0.1551	-0.2415	-0.1376	0.1716	0.0082	0.2089	0.051	-0.2365	-0.2013	-0.0148	-0.1193	3.739	40.589	40.362

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	1 - 169	21 - 189
2	1	349 - 371	369 - 391
3	2	170 - 348	190 - 368

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi