PDB-2x0d: APO structure of WsaF

ID or keywords:

Entry

Database: PDB / ID: 2x0d

Title

APO structure of WsaF

Components

WSAF

Keywords

TRANSFERASE / GT4 FAMILY

Function / homology

Function and homology information

polysaccharide binding
Similarity search - Function

Biological species

GEOBACILLUS STEAROTHERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.28 Å

Authors

Steiner, K. / Hagelueken, G. / Naismith, J.H.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Structural Basis of Substrate Binding in Wsaf, a Rhamnosyltransferase from Geobacillus Stearothermophilus.
Authors: Steiner, K. / Hagelueken, G. / Messner, P. / Schaeffer, C. / Naismith, J.H.

History

Deposition	Dec 8, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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

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Download

PDBx/mmCIF format	2x0d.cif.gz	167.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2x0d.ent.gz	134.5 KB	Display	PDB format
PDBx/mmJSON format	2x0d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/2x0d ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x0d	HTTPS FTP

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Related structure data

Related structure data	2x0eC 2x0fC C: citing same article (ref.)
Similar structure data	2x0e-d 2x0f-d 4mr0-d 5zmd-2 4ija-d 5jil-1 5thz-d 4a4m-1 5zmd-1 1z6r-2 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: WSAF

B: WSAF

hetero molecules

97.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	75.987, 75.482, 78.059
Angle α, β, γ (deg.)	90.00, 103.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B

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	GLU	GLU	PRO	PRO	2	A	A	33 - 54	33 - 54
2	1	1	GLU	GLU	PRO	PRO	2	B	B	33 - 54	33 - 54
1	2	1	GLY	GLY	GLU	GLU	2	A	A	64 - 73	64 - 73
2	2	1	GLY	GLY	GLU	GLU	2	B	B	64 - 73	64 - 73
1	3	1	LYS	LYS	PRO	PRO	2	A	A	79 - 91	79 - 91
2	3	1	LYS	LYS	PRO	PRO	2	B	B	79 - 91	79 - 91
1	4	1	GLN	GLN	ASP	ASP	2	A	A	97 - 122	97 - 122
2	4	1	GLN	GLN	ASP	ASP	2	B	B	97 - 122	97 - 122
1	5	1	ARG	ARG	ASN	ASN	6	A	A	123 - 125	123 - 125
2	5	1	ARG	ARG	ASN	ASN	6	B	B	123 - 125	123 - 125
1	6	1	ARG	ARG	PRO	PRO	2	A	A	126 - 224	126 - 224
2	6	1	ARG	ARG	PRO	PRO	2	B	B	126 - 224	126 - 224
1	7	1	PHE	PHE	LEU	LEU	5	A	A	403 - 413	403 - 413
2	7	1	PHE	PHE	LEU	LEU	5	B	B	403 - 413	403 - 413
1	1	2	ILE	ILE	ILE	ILE	2	A	A	226 - 234	226 - 234
2	1	2	ILE	ILE	ILE	ILE	2	B	B	226 - 234	226 - 234
1	1	3	ILE	ILE	ILE	ILE	2	A	A	279 - 289	279 - 289
2	1	3	ILE	ILE	ILE	ILE	2	B	B	279 - 289	279 - 289
1	1	4	ASN	ASN	LYS	LYS	2	A	A	235 - 278	235 - 278
2	1	4	ASN	ASN	LYS	LYS	2	B	B	235 - 278	235 - 278
1	2	4	ALA	ALA	LEU	LEU	2	A	A	290 - 300	290 - 300
2	2	4	ALA	ALA	LEU	LEU	2	B	B	290 - 300	290 - 300
1	3	4	SER	SER	ASN	ASN	2	A	A	316 - 381	316 - 381
2	3	4	SER	SER	ASN	ASN	2	B	B	316 - 381	316 - 381
1	1	5	SER	SER	GLY	GLY	5	A	A	55 - 63	55 - 63
2	1	5	SER	SER	GLY	GLY	5	B	B	55 - 63	55 - 63

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	WSAF / RHAMNOSYLTRANSFERASE Mass: 48780.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Strain: 2004/3A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7BG50
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.91 % / Description: NONE
Crystal grow	Details: 18%(W/V) PEG 3350, 0.22M AMMONIUM CHLORIDE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9764
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9764 Å / Relative weight: 1
Reflection	Resolution: 2.28→47.3 Å / Num. obs: 39051 / % possible obs: 99.9 % / Observed criterion σ(I): 3.3 / Redundancy: 14.4 % / R_merge(I) obs: 0.16 / Net I/σ(I): 14.1
Reflection shell	Resolution: 2.28→2.34 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 3.3 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX	AUTOSOLVE	phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.28→47.14 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.917 / SU B: 15.915 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	1994	5.1 %	RANDOM
R_work	0.19	-	-	-
obs	0.193	37017	98.9 %	-

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: 32.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	-0 Å²	0.2 Å²
2-	-	-0.3 Å²	-0 Å²
3-	-	-	0.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→47.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6236	0	18	176	6430

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	6451
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.205	1.956	8727
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.143	5	766
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.875	24.628	309
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.162	15	1171
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.887	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	940
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4860
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1310
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	1193
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	4424
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	3032
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	3284
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.123	0.2	203
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	0.136	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.229	0.2	17
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.252	0.2	7
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	0.485	1.5	3813
X-RAY DIFFRACTION	r_mcbond_other	0.085	1.5	1504
X-RAY DIFFRACTION	r_mcangle_it	0.924	2	6221
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.449	3	2638
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.429	4.5	2499
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	999	tight positional	0.03	0.05
1	2	B	999	tight positional	0.03	0.05
2	1	A	54	tight positional	0.03	0.05
2	2	B	54	tight positional	0.03	0.05
3	1	A	65	tight positional	0.02	0.05
3	2	B	65	tight positional	0.02	0.05
4	1	A	709	tight positional	0.03	0.05
4	2	B	709	tight positional	0.03	0.05
1	1	A	1477	medium positional	0.37	0.5
1	2	B	1477	medium positional	0.37	0.5
2	1	A	68	medium positional	0.27	0.5
2	2	B	68	medium positional	0.27	0.5
3	1	A	82	medium positional	0.29	0.5
3	2	B	82	medium positional	0.29	0.5
4	1	A	952	medium positional	0.22	0.5
4	2	B	952	medium positional	0.22	0.5
5	1	A	53	medium positional	0.17	0.5
5	2	B	53	medium positional	0.17	0.5
1	1	A	163	loose positional	0.6	5
1	2	B	163	loose positional	0.6	5
5	1	A	69	loose positional	0.99	5
5	2	B	69	loose positional	0.99	5
1	1	A	999	tight thermal	0.06	0.5
1	2	B	999	tight thermal	0.06	0.5
2	1	A	54	tight thermal	0.05	0.5
2	2	B	54	tight thermal	0.05	0.5
3	1	A	65	tight thermal	0.05	0.5
3	2	B	65	tight thermal	0.05	0.5
4	1	A	709	tight thermal	0.06	0.5
4	2	B	709	tight thermal	0.06	0.5
1	1	A	1477	medium thermal	0.28	2
1	2	B	1477	medium thermal	0.28	2
2	1	A	68	medium thermal	0.24	2
2	2	B	68	medium thermal	0.24	2
3	1	A	82	medium thermal	0.24	2
3	2	B	82	medium thermal	0.24	2
4	1	A	952	medium thermal	0.27	2
4	2	B	952	medium thermal	0.27	2
5	1	A	53	medium thermal	0.16	2
5	2	B	53	medium thermal	0.16	2
1	1	A	163	loose thermal	0.65	10
1	2	B	163	loose thermal	0.65	10
5	1	A	69	loose thermal	0.3	10
5	2	B	69	loose thermal	0.3	10

LS refinement shell

Resolution: 2.28→2.34 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.288	137	-
R_work	0.254	2547	-
obs	-	-	93.36 %

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	3.8059	2.1137	-6.612	8.6766	8.0162	29.6979	0.6661	0.436	0.889	-0.8037	0.3408	0.8498	-3.0421	-0.5429	-1.0069	0.6315	-0.0607	-0.0546	0.437	0.1721	0.4812	12.655	50.917	66.831
2	4.9091	0.5765	1.242	1.3236	-0.046	2.1791	0.0185	-0.6105	0.0749	0.2504	-0.05	-0.0842	-0.0534	0.0735	0.0316	0.0832	0.0049	-0.0011	0.1107	-0.0132	0.022	13.296	38.445	83.011
3	3.2862	-0.4384	-0.7703	1.9604	-0.1264	2.9458	0.0272	-0.187	-0.0863	0.1473	-0.0095	0.0853	0.0207	-0.1206	-0.0176	0.055	-0.0037	0.0058	0.06	0.006	0.0062	-19.81	38.591	82.368
4	0.674	-1.3195	-1.0016	5.9376	-3.1628	9.3385	0.5472	0.0647	0.1934	-0.0234	-0.0718	-0.2154	-1.9787	-0.1242	-0.4753	0.7133	-0.1727	0.1626	0.2925	-0.0138	0.2222	-18.068	51.077	63.746
5	3.3801	-0.5321	1.5386	1.5222	-0.2368	2.4829	-0.0202	0.2907	0.0033	-0.2482	-0.0528	0.0726	-0.0426	-0.012	0.073	0.0833	-0.0161	-0.0053	0.0521	-0.0024	0.0168	-18.661	40.093	46.504
6	4.3247	0.8694	-0.0368	2.2082	0.1731	2.865	-0.0185	0.4332	-0.0702	-0.2095	0.0564	-0.1154	-0.0255	0.1515	-0.0379	0.0612	0.0142	0.0045	0.0916	-0.0135	0.0083	14.466	40.572	47.129

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 37
2	X-RAY DIFFRACTION	2	A	38 - 222
3	X-RAY DIFFRACTION	2	A	398 - 413
4	X-RAY DIFFRACTION	3	A	223 - 397
5	X-RAY DIFFRACTION	4	B	26 - 37
6	X-RAY DIFFRACTION	5	B	38 - 222
7	X-RAY DIFFRACTION	5	B	398 - 413
8	X-RAY DIFFRACTION	6	B	223 - 397

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