PDB-2bo7: DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLT...

ID or keywords:

Entry

Database: PDB / ID: 2bo7

Title

DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE

Components

MANNOSYLGLYCERATE SYNTHASE

Keywords

TRANSFERASE / CATALYSIS / GLYCOSYLTRANSFERASE / MANNOSE / STEREOSELECTIVITY

Function / homology

Function and homology information

mannosylglycerate synthase / mannosylglycerate synthase activity / mannosylglycerate biosynthetic process / hexosyltransferase activity / metal ion binding / identical protein binding
Similarity search - Function

Biological species

RHODOTHERMUS MARINUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

Flint, J. / Taylor, E. / Yang, M. / Bolam, D.N. / Tailford, L.E. / Martinez-Fleites, C. / Dodson, E.J. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.

Citation

Journal: Nat. Struct. Mol. Biol. / Year: 2005
Title: Structural dissection and high-throughput screening of mannosylglycerate synthase.
Authors: Flint, J. / Taylor, E. / Yang, M. / Bolam, D.N. / Tailford, L.E. / Martinez-Fleites, C. / Dodson, E.J. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.

History

Deposition	Apr 8, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 6, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jan 16, 2019	Group: Data collection / Database references / Derived calculations Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_prop Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_assembly.method_details
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2bo7.cif.gz	731.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2bo7.ent.gz	602.7 KB	Display	PDB format
PDBx/mmJSON format	2bo7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2bo7_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	2bo7_full_validation.pdf.gz	4.5 MB	Display
Data in XML	2bo7_validation.xml.gz	130.5 KB	Display
Data in CIF	2bo7_validation.cif.gz	172.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/2bo7 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2bo7	HTTPS FTP

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Related structure data

Related structure data	2bo4C 2bo6SC 2bo8C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2bo8-3 2bo8-1 2bo8-2 2bo4-2 2bo4-1 2bo6-1 4hb0-d 3v77-d 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

2bo4C

2bo6SC

2bo8C

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: MANNOSYLGLYCERATE SYNTHASE

B: MANNOSYLGLYCERATE SYNTHASE

C: MANNOSYLGLYCERATE SYNTHASE

D: MANNOSYLGLYCERATE SYNTHASE

E: MANNOSYLGLYCERATE SYNTHASE

F: MANNOSYLGLYCERATE SYNTHASE

G: MANNOSYLGLYCERATE SYNTHASE

H: MANNOSYLGLYCERATE SYNTHASE

I: MANNOSYLGLYCERATE SYNTHASE

J: MANNOSYLGLYCERATE SYNTHASE

hetero molecules

467 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MANNOSYLGLYCERATE SYNTHASE

B: MANNOSYLGLYCERATE SYNTHASE

C: MANNOSYLGLYCERATE SYNTHASE

D: MANNOSYLGLYCERATE SYNTHASE

hetero molecules

defined by author&software
187 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: MANNOSYLGLYCERATE SYNTHASE

F: MANNOSYLGLYCERATE SYNTHASE

G: MANNOSYLGLYCERATE SYNTHASE

H: MANNOSYLGLYCERATE SYNTHASE

hetero molecules

defined by author&software
187 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: MANNOSYLGLYCERATE SYNTHASE

J: MANNOSYLGLYCERATE SYNTHASE

hetero molecules

I: MANNOSYLGLYCERATE SYNTHASE

J: MANNOSYLGLYCERATE SYNTHASE

hetero molecules

defined by author&software
187 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	406.699, 162.140, 108.431
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	2 - 500
2	1	1	1	B	2 - 500
3	1	1	1	C	2 - 500
4	1	1	1	D	2 - 500
5	1	1	1	E	2 - 500
6	1	1	1	F	2 - 500
7	1	1	1	G	2 - 500
8	1	1	1	H	2 - 500
9	1	1	1	I	2 - 500
10	1	1	1	J	2 - 500

#1: Protein	MANNOSYLGLYCERATE SYNTHASE Mass: 46186.473 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER References: UniProt: Q9RFR0, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Co
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.5 Å³/Da / Density % sol: 72.2 %
Crystal grow	Details: 10 MM NACL, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 15% (V/V) MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.95→40 Å / Num. obs: 151344 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / R_merge(I) obs: 0.1 / Net I/σ(I): 13
Reflection shell	Resolution: 2.95→3.11 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 93

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0003	refinement
HKL		data reduction
HKL		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BO6

2bo6

Resolution: 2.95→223.61 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.919 / SU B: 29.694 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.915 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	7443	5 %	RANDOM
R_work	0.207	-	-	-
obs	0.208	140625	97.8 %	-

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: 63.38 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	0 Å²
2-	-	0.71 Å²	0 Å²
3-	-	-	-0.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→223.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31020	0	290	127	31437

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	32210
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.439	1.932	43880
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.297	5	3730
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.299	22.143	1680
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.176	15	5140
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.077	15	350
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	4650
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	25080
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	14455
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.322	0.2	22007
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	933
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	0.468	0.2	190
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.437	0.2	11
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	0.289	1.5	18987
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.39	2	30280
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.76	3	15115
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.042	4.5	13600
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 3131 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.07	0.05
2	B	tight positional	0.07	0.05
3	C	tight positional	0.06	0.05
4	D	tight positional	0.06	0.05
5	E	tight positional	0.06	0.05
6	F	tight positional	0.03	0.05
7	G	tight positional	0.04	0.05
8	H	tight positional	0.03	0.05
9	I	tight positional	0.04	0.05
10	J	tight positional	0.04	0.05
1	A	tight thermal	0.13	0.5
2	B	tight thermal	0.13	0.5
3	C	tight thermal	0.08	0.5
4	D	tight thermal	0.09	0.5
5	E	tight thermal	0.1	0.5
6	F	tight thermal	0.07	0.5
7	G	tight thermal	0.07	0.5
8	H	tight thermal	0.06	0.5
9	I	tight thermal	0.06	0.5
10	J	tight thermal	0.07	0.5

LS refinement shell

Resolution: 2.95→3.03 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.359	443
R_work	0.324	9237

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	2.1058	0.4578	-0.0183	2.2083	-0.5964	1.5674	-0.0142	-0.0872	0.0318	-0.005	0.0152	0.173	0.2593	-0.1073	-0.0011	-0.2239	0.0578	0.0388	-0.4613	-0.0194	-0.4357	94.182	30.298	16.584
2	1.4347	-0.3944	0.8159	2.9062	-1.0388	2.8447	-0.0558	0.1838	-0.1168	-0.1519	0.0445	-0.0188	-0.1395	0.0863	0.0113	-0.3458	-0.0285	0.0407	-0.4716	-0.0208	-0.4188	93.434	74.65	-1.405
3	2.157	-0.2683	0.0858	2.391	1.5	2.9805	0.214	0.146	0.0895	-0.0558	-0.1585	0.1536	-0.035	-0.5154	-0.0556	-0.4055	0.1115	0.0887	-0.0812	0.0086	-0.1385	55.197	64.884	5.567
4	2.8643	-0.3741	-1.0975	1.2846	-0.0328	2.3215	0.064	0.3557	-0.193	-0.2001	-0.1598	0.2318	0.5321	-0.339	0.0958	-0.082	-0.0467	-0.0473	-0.0643	-0.1543	-0.2733	73.688	27.572	-18.02
5	1.7298	-0.032	0.1257	2.556	0.445	2.3146	-0.0554	-0.2049	0.0241	0.0071	-0.0775	-0.1685	-0.1818	0.0417	0.1329	-0.0917	0.1412	0.0156	-0.1459	0.0495	-0.4466	111.731	31.477	49.256
6	5.5554	0.7385	0.6942	1.7572	-0.282	2.1991	-0.0352	-0.321	1.4834	0.0723	-0.1927	-0.3142	-0.9852	0.264	0.2278	0.8558	-0.1453	-0.0961	0.0625	0.0672	0.4308	137.384	71.91	50.687
7	5.6143	-0.9818	0.1408	1.5458	-0.258	1.9161	0.0324	-0.8978	0.101	0.082	-0.1794	-0.2365	-0.2101	-0.1235	0.147	-0.0416	-0.0455	0.019	0.3978	0.0607	-0.356	129.16	32.26	85.339
8	2.345	-0.2956	-0.3462	1.2561	-0.3844	3.4227	0.0988	0.1413	0.2458	-0.1417	-0.1049	-0.1215	-0.3975	0.3437	0.0061	0.0897	-0.21	0.0424	0.4459	0.2933	0.0846	164.058	42.003	54.178
9	2.4548	-0.0409	-0.2777	2.0983	-0.8001	2.3064	0.2198	0.3991	0.0898	-0.2482	-0.1264	-0.0798	-0.0688	0.4112	-0.0934	-0.2058	-0.1414	0.0351	0.6919	0.1514	0.0206	189.425	14.492	56.168
10	3.7565	-1.44	0.3903	2.3737	-0.6884	1.8193	-0.0113	-0.2201	-0.4396	0.1421	0.13	0.1352	0.2161	0.4229	-0.1187	-0.3565	-0.1604	0.0676	0.3214	0.1106	0.1559	184.943	-7.892	98.418

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 382
2	X-RAY DIFFRACTION	2	B	2 - 382
3	X-RAY DIFFRACTION	3	C	2 - 382
4	X-RAY DIFFRACTION	4	D	2 - 382
5	X-RAY DIFFRACTION	5	E	2 - 382
6	X-RAY DIFFRACTION	6	F	2 - 382
7	X-RAY DIFFRACTION	7	G	2 - 382
8	X-RAY DIFFRACTION	8	H	2 - 382
9	X-RAY DIFFRACTION	9	I	2 - 382
10	X-RAY DIFFRACTION	10	J	2 - 382

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