PDB-3tzt: The structure of a protein in glycosyl transferase family 8 from ...

ID or keywords:

Entry

Database: PDB / ID: 3tzt

Title

The structure of a protein in glycosyl transferase family 8 from Anaerococcus prevotii.

Components

Glycosyl transferase family 8

Keywords

TRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / putative glycosyl transferase / general stress protein

Function / homology

Function and homology information

glycosyltransferase activity
Similarity search - Function

Biological species

Anaerococcus prevotii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Cuff, M.E. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a protein in glycosyl transferase family 8 from Anaerococcus prevotii.
Authors: Cuff, M.E. / Tesar, C. / Bearden, J. / Joachimiak, A.

History

Deposition	Sep 27, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Structure summary
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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	3tzt.cif.gz	215.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3tzt.ent.gz	172 KB	Display	PDB format
PDBx/mmJSON format	3tzt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tzt_validation.pdf.gz	468 KB	Display	wwPDB validaton report
Full document	3tzt_full_validation.pdf.gz	474.1 KB	Display
Data in XML	3tzt_validation.xml.gz	25.4 KB	Display
Data in CIF	3tzt_validation.cif.gz	34.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tz/3tzt ftp://data.pdbj.org/pub/pdb/validation_reports/tz/3tzt	HTTPS FTP

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Related structure data

Similar structure data	6qbq-d 6qbr-d 3lez-2 5j1b-d 3p23-5 4eg5-2 6qbp-d 6qbn-d 5vid-2 6qbo-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
Other databases	TargetDB: APC100377

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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)

Deposited unit

A: Glycosyl transferase family 8

B: Glycosyl transferase family 8

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	42.498, 99.331, 122.794
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

Likely the AB dimer in the AU.

#1: Protein	Glycosyl transferase family 8 Mass: 32823.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaerococcus prevotii (bacteria) / Strain: DSM 20548 / Gene: Apre_0416 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C7RG54
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.97 Å³/Da / Density % sol: 37.69 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2M Amonium citrate dibasic, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918, 0.97929

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97918	1
2	0.97929	1

Reflection

Redundancy: 7.1 % / Av σ(I) over netI: 27.44 / Number: 224942 / R_merge(I) obs: 0.062 / Χ²: 0.89 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 31606 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.7	50	97.1	1	0.037	0.836	6.2
4.52	5.7	99.9	1	0.038	0.732	6.7
3.95	4.52	100	1	0.045	0.979	6.8
3.59	3.95	99.9	1	0.049	0.997	7
3.33	3.59	100	1	0.049	0.843	7.1
3.14	3.33	100	1	0.054	0.784	7.2
2.98	3.14	100	1	0.065	0.81	7.2
2.85	2.98	100	1	0.073	0.812	7.3
2.74	2.85	100	1	0.095	0.886	7.3
2.65	2.74	100	1	0.114	0.912	7.3
2.56	2.65	100	1	0.143	0.896	7.3
2.49	2.56	100	1	0.172	0.936	7.3
2.42	2.49	100	1	0.192	0.949	7.3
2.37	2.42	100	1	0.23	0.941	7.3
2.31	2.37	100	1	0.262	0.927	7.2
2.26	2.31	100	1	0.315	0.939	7.3
2.22	2.26	100	1	0.36	0.947	7.2
2.18	2.22	100	1	0.427	0.897	7.3
2.14	2.18	99.9	1	0.51	0.911	7.2
2.1	2.14	99.9	1	0.588	0.897	7.1

Reflection

Resolution: 2.1→50 Å / Num. all: 31606 / Num. obs: 31606 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / B_iso Wilson estimate: 25.1 Å² / R_merge(I) obs: 0.062 / Χ²: 0.892 / Net I/σ(I): 10.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.14	7.1	0.588	1589	0.897	1	99.9
2.14-2.18	7.2	0.51	1520	0.911	1	99.9
2.18-2.22	7.3	0.427	1552	0.897	1	100
2.22-2.26	7.2	0.36	1543	0.947	1	100
2.26-2.31	7.3	0.315	1554	0.939	1	100
2.31-2.37	7.2	0.262	1584	0.927	1	100
2.37-2.42	7.3	0.23	1539	0.941	1	100
2.42-2.49	7.3	0.192	1557	0.949	1	100
2.49-2.56	7.3	0.172	1574	0.936	1	100
2.56-2.65	7.3	0.143	1567	0.896	1	100
2.65-2.74	7.3	0.114	1558	0.912	1	100
2.74-2.85	7.3	0.095	1575	0.886	1	100
2.85-2.98	7.3	0.073	1567	0.812	1	100
2.98-3.14	7.2	0.065	1577	0.81	1	100
3.14-3.33	7.2	0.054	1598	0.784	1	100
3.33-3.59	7.1	0.049	1593	0.843	1	100
3.59-3.95	7	0.049	1598	0.997	1	99.9
3.95-4.52	6.8	0.045	1614	0.979	1	100
4.52-5.7	6.7	0.038	1642	0.732	1	99.9
5.7-50	6.2	0.037	1705	0.836	1	97.1

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.1 Å / D res low: 50 Å / FOM : 0.347 / FOM acentric: 0.371 / FOM centric: 0.164 / Reflection: 30355 / Reflection acentric: 26744 / Reflection centric: 3611

Phasing MAD set

Highest resolution: 2.1 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.49	1	0.3	0.3	0	0	26744	3611
2	0.97	0.94	37.7	53.2	0.38	0.31	17064	2636

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.98-50	1.05	1	0.7	0.6	0	0	72	73
1	7.46-12.98	1.14	1	0.9	0.7	0	0	419	182
1	5.23-7.46	1.57	1	0.7	0.4	0	0	1085	304
1	4.03-5.23	1.07	1	0.6	0.5	0	0	2045	419
1	3.28-4.03	1.2	1	0.4	0.3	0	0	3289	524
1	2.76-3.28	1.89	1	0.4	0.2	0	0	4866	643
1	2.39-2.76	2.25	1	0.2	0.1	0	0	6726	746
1	2.1-2.39	1.62	1	0.1	0	0	0	8242	720
2	12.98-50	0.92	0.9	55.6	60.8	0.71	0.63	68	68
2	7.46-12.98	0.91	0.89	54.9	57.3	0.61	0.55	417	178
2	5.23-7.46	0.93	0.87	38	47.6	0.74	0.55	1085	304
2	4.03-5.23	0.96	0.94	50.1	66.2	0.45	0.32	2045	419
2	3.28-4.03	0.98	0.95	44.6	62.5	0.36	0.24	3289	524
2	2.76-3.28	0.98	0.96	33.5	45.7	0.35	0.22	4866	643
2	2.39-2.76	0.99	0.98	30.8	42.9	0.26	0.15	5294	500
2	2.1-2.39	0	0	0	0	0	0	0	0

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	21.7385	0.207	0.4	0.142	7.337	0
2	27.1598	0.037	0.369	0.187	8.417	0
3	19.1715	-0.322	0.409	0.172	6.156	0
4	22.9331	-0.151	0.447	0.131	6.679	0
5	29.882	0.257	0.4	0.017	5.067	0
6	21.0161	-0.438	0.261	0.183	4.799	0
7	34.8677	-0.312	0.247	0.161	4.382	0
8	23.8419	-0.214	0.283	0.242	4.498	0
9	33.9147	0.084	0.492	0.046	4.093	0
10	41.0733	0.122	0.384	0.015	3.72	0
11	39.1673	-0.367	0.156	0.38	4.386	0
12	66.7456	0.272	0.393	-0.095	2.032	0
13	15.7467	0.206	0.399	0.141	4.358	-0.192
14	23.0023	0.037	0.368	0.188	4.795	-0.243
15	16.7049	-0.324	0.407	0.172	3.432	-0.17
16	23.6521	-0.152	0.447	0.132	4.206	-0.226
17	41.5724	0.255	0.398	0.017	2.284	-0.276
18	22.3385	-0.437	0.261	0.18	2.438	-0.243
19	31.451	-0.313	0.247	0.161	2.52	-0.168
20	15.7014	-0.212	0.282	0.241	2.916	-0.114
21	43.6228	0.081	0.492	0.046	3.041	-0.231
22	101.4886	0.124	0.384	0.016	3.095	-0.206
23	39.662	-0.362	0.153	0.382	2.698	-0.193
24	51.364	0.266	0.392	-0.096	1.045	-0.116

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.98-50	0.443	0.574	0.314	145	72	73
7.46-12.98	0.539	0.642	0.303	601	419	182
5.23-7.46	0.623	0.696	0.364	1389	1085	304
4.03-5.23	0.548	0.609	0.249	2464	2045	419
3.28-4.03	0.535	0.585	0.221	3813	3289	524
2.76-3.28	0.484	0.523	0.193	5509	4866	643
2.39-2.76	0.305	0.33	0.08	7472	6726	746
2.1-2.39	0.105	0.114	0	8962	8242	720

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 30355

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.43-100	64.6	0.52	508
6.74-8.43	51.8	0.866	506
5.8-6.74	47.7	0.893	566
5.17-5.8	43.8	0.916	639
4.71-5.17	49.4	0.917	694
4.35-4.71	48.6	0.936	766
4.06-4.35	55	0.922	816
3.83-4.06	52.9	0.923	848
3.63-3.83	50.7	0.919	914
3.46-3.63	52	0.908	964
3.31-3.46	57.1	0.9	995
3.18-3.31	54.2	0.899	1031
3.06-3.18	56.5	0.884	1077
2.95-3.06	53.9	0.885	1109
2.86-2.95	56.4	0.889	1135
2.77-2.86	59.3	0.867	1178
2.69-2.77	61	0.854	1230
2.62-2.69	62.5	0.843	1240
2.55-2.62	64.9	0.808	1279
2.49-2.55	64.6	0.823	1300
2.44-2.49	70.1	0.83	1378
2.38-2.44	72.6	0.832	1351
2.33-2.38	75.1	0.811	1387
2.28-2.33	81	0.818	1428
2.24-2.28	78.5	0.813	1375
2.2-2.24	82.4	0.813	1414
2.16-2.2	83	0.774	1324
2.1-2.16	86	0.739	1903

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
COO		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.1→37.84 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.935 / WR_factor R_free: 0.2122 / WR_factor R_work: 0.1592 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9134 / SU B: 7.167 / SU ML: 0.096 / SU R Cruickshank DPI: 0.2045 / SU R_free: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2059	1518	5 %	RANDOM
R_work	0.1594	-	-	-
all	0.1617	30241	-	-
obs	0.1617	30241	96.88 %	-

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 max: 113.89 Å² / B_iso mean: 35.7841 Å² / B_iso min: 11.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	0 Å²
2-	-	-0.09 Å²	0 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→37.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3839	0	41	263	4143

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	4028
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2775
X-RAY DIFFRACTION	r_angle_refined_deg	1.59	1.99	5451
X-RAY DIFFRACTION	r_angle_other_deg	0.963	3	6736
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.258	5	475
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.748	23.568	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.207	15	712
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.638	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	595
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	4390
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	843

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.234	82	-
R_work	0.19	1598	-
all	-	1680	-
obs	-	-	78.14 %

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	0.5641	0.5366	-0.2945	1.4463	-0.7739	1.6431	0.0567	-0.05	-0.0746	0.0345	-0.0842	-0.0032	0.024	-0.0041	0.0275	0.0318	0.0356	-0.002	0.0851	-0.0078	0.0965	-2.9698	29.0854	23.2813
2	0.7558	0.5379	-0.331	1.5332	-0.5675	1.1196	0.027	0.0989	0.1187	-0.2249	0.0303	0.1255	-0.1056	-0.1088	-0.0573	0.1211	0.0802	-0.0014	0.1013	0.0031	0.0935	-3.6867	43.3929	8.5227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999

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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

-
Phasing

-
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