PDB-9gph: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with m...

ID or keywords:

Entry

Database: PDB / ID: 9gph

Title

Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (-1) and phosphate

Components

1,2-beta-oligomannan phosphorylase

Keywords

CARBOHYDRATE / phosphorylase

Function / homology

1,2-beta-oligomannan phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / GDP-mannose biosynthetic process / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / alpha-D-mannopyranose / PHOSPHATE ION / 1,2-beta-oligomannan phosphorylase

Function and homology information

Biological species

Thermoanaerobacter sp. X514 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Cioci, G. / Durand, J. / Veronese-Potocki, G. / Ladeveze, S.

Funding support

1items

Citation

Journal: To Be Published
Title: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (-1) and phosphate
Authors: Cioci, G. / Durand, J. / Veronese-Potocki, G. / Ladeveze, S.

History

Deposition	Sep 7, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9gph.cif.gz	276.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9gph.ent.gz	214.7 KB	Display	PDB format
PDBx/mmJSON format	9gph.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9gph_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	9gph_full_validation.pdf.gz	3 MB	Display
Data in XML	9gph_validation.xml.gz	43.7 KB	Display
Data in CIF	9gph_validation.cif.gz	60.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gp/9gph ftp://data.pdbj.org/pub/pdb/validation_reports/gp/9gph	HTTPS FTP

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Related structure data

Related structure data	9gqsC C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

A: 1,2-beta-oligomannan phosphorylase

B: 1,2-beta-oligomannan phosphorylase

C: 1,2-beta-oligomannan phosphorylase

D: 1,2-beta-oligomannan phosphorylase

hetero molecules

141 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.386, 67.570, 299.540
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	2 - 296	2 - 296
2	1	1	LYS	LYS	2 - 296	2 - 296
3	2	2	HIS	HIS	2 - 303	2 - 303
4	2	2	HIS	HIS	2 - 303	2 - 303
5	3	3	HIS	HIS	2 - 303	2 - 303
6	3	3	HIS	HIS	2 - 303	2 - 303
7	4	4	LYS	LYS	2 - 296	2 - 296
8	4	4	LYS	LYS	2 - 296	2 - 296
9	5	5	LYS	LYS	2 - 296	2 - 296
10	5	5	LYS	LYS	2 - 296	2 - 296
11	6	6	HIS	HIS	2 - 303	2 - 303
12	6	6	HIS	HIS	2 - 303	2 - 303

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein

1,2-beta-oligomannan phosphorylase / 1 / 2-beta-oligomannan:phosphate alpha-D-mannosyltransferase

Mass: 34927.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermoanaerobacter sp. X514 (bacteria) / Gene: Teth514_1788 / Production host:

Escherichia coli (E. coli)
References: UniProt: B0K2C2, 1,2-beta-oligomannan phosphorylase

#2: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION

#3: Sugar

ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.6 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: to be retrieved

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.03987 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03987 Å / Relative weight: 1
Reflection	Resolution: 1.7→50.005 Å / Num. obs: 150586 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC_1/2: 0.971 / Net I/σ(I): 2
Reflection shell	Resolution: 1.7→1.79 Å / Num. unique obs: 20773 / CC_1/2: 0.731

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→50.005 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.95 / SU B: 2.954 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / ESU R: 0.108 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2157	7453	4.954 %
R_work	0.1919	142981	-
all	0.193	-	-
obs	-	150434	99.349 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.233 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.513 Å²	0 Å²	0 Å²
2-	-	0.785 Å²	0 Å²
3-	-	-	-2.298 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→50.005 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9752	0	96	809	10657

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	10116
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9499
X-RAY DIFFRACTION	r_angle_refined_deg	1.521	1.832	13704
X-RAY DIFFRACTION	r_angle_other_deg	0.532	1.782	21933
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.688	5	1200
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.495	5	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.735	10	1719
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.459	10	481
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1443
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11754
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2294
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	1479
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	8803
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	4735
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	5005
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	661
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.159	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.164	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	22
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.022	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.945	2.257	4809
X-RAY DIFFRACTION	r_mcbond_other	1.944	2.257	4809
X-RAY DIFFRACTION	r_mcangle_it	2.624	4.045	6006
X-RAY DIFFRACTION	r_mcangle_other	2.624	4.046	6007
X-RAY DIFFRACTION	r_scbond_it	3.049	2.611	5307
X-RAY DIFFRACTION	r_scbond_other	3.048	2.611	5308
X-RAY DIFFRACTION	r_scangle_it	4.647	4.62	7698
X-RAY DIFFRACTION	r_scangle_other	4.647	4.62	7699
X-RAY DIFFRACTION	r_lrange_it	5.623	23.225	10901
X-RAY DIFFRACTION	r_lrange_other	5.553	22.886	10715
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	10015
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.081	0.05	10252
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.059	0.05	10397
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.065	0.05	10137
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.084	0.05	9892
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.082	0.05	10170

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07685	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07685	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08119	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08119	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05861	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05861	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06505	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06505	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08428	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08428	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08219	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.08219	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.7-1.744	0.304	552	0.313	10420	0.312	11019	0.917	0.917	99.5735	0.315
1.744-1.792	0.29	529	0.284	10233	0.284	10806	0.929	0.935	99.5928	0.285
1.792-1.844	0.285	556	0.261	9937	0.263	10511	0.939	0.947	99.8288	0.259
1.844-1.9	0.26	476	0.241	9654	0.242	10159	0.952	0.956	99.7145	0.238
1.9-1.963	0.269	470	0.228	9427	0.23	9916	0.953	0.963	99.8084	0.225
1.963-2.031	0.254	466	0.222	9110	0.223	9613	0.956	0.966	99.6151	0.218
2.031-2.108	0.226	479	0.206	8703	0.207	9240	0.965	0.972	99.3723	0.204
2.108-2.194	0.228	370	0.201	8455	0.202	8897	0.965	0.974	99.1907	0.2
2.194-2.291	0.226	420	0.185	8083	0.187	8552	0.968	0.978	99.427	0.185
2.291-2.403	0.204	427	0.181	7783	0.183	8235	0.973	0.979	99.6964	0.184
2.403-2.532	0.224	396	0.182	7357	0.184	7771	0.965	0.979	99.7684	0.188
2.532-2.686	0.212	373	0.184	7019	0.185	7429	0.972	0.979	99.502	0.193
2.686-2.87	0.226	356	0.182	6572	0.185	6960	0.971	0.979	99.5402	0.195
2.87-3.1	0.191	327	0.182	6159	0.182	6527	0.976	0.98	99.3718	0.2
3.1-3.394	0.215	294	0.192	5683	0.193	6024	0.971	0.978	99.2198	0.212
3.394-3.793	0.211	247	0.19	5192	0.191	5487	0.975	0.98	99.1252	0.215
3.793-4.375	0.175	250	0.157	4518	0.158	4839	0.982	0.985	98.5328	0.188
4.375-5.348	0.156	213	0.141	3858	0.142	4161	0.987	0.99	97.8371	0.176
5.348-7.521	0.18	162	0.176	3034	0.176	3310	0.982	0.986	96.5559	0.21
7.521-50.005	0.249	90	0.171	1785	0.174	1954	0.971	0.983	95.957	0.206

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