PDB-4hes: Structure of a Beta-Lactamase Class A-like Protein from Veillonel...

ID or keywords:

Entry

Database: PDB / ID: 4hes

Title

Structure of a Beta-Lactamase Class A-like Protein from Veillonella parvula.

Components

Beta-lactamase class A-like protein

Keywords

HYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Beta-lactamase class A-like / COG COG2367

Function / homology

Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Beta-lactamase class A-like protein

Function and homology information

Biological species

Veillonella parvula (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Cuff, M.E. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of a Beta-Lactamase Class A-like Protein from Veillonella parvula.
Authors: Cuff, M.E. / Li, H. / Clancy, S. / Joachimiak, A.

History

Deposition	Oct 4, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Nov 6, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr1_label_comp_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_atom_id / _struct_conn.ptnr2_label_comp_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	4hes.cif.gz	578.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4hes.ent.gz	478.3 KB	Display	PDB format
PDBx/mmJSON format	4hes.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hes_validation.pdf.gz	483.9 KB	Display	wwPDB validaton report
Full document	4hes_full_validation.pdf.gz	492.6 KB	Display
Data in XML	4hes_validation.xml.gz	74.9 KB	Display
Data in CIF	4hes_validation.cif.gz	105 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/4hes ftp://data.pdbj.org/pub/pdb/validation_reports/he/4hes	HTTPS FTP

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Related structure data

Similar structure data	3fru-2 6qga-1 6dsr-d 4tlv-1 6qz2-9 6qgb-2 3ln5-d 4pfu-1 4wpt-d 5g62-1 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-apc100815

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-lactamase class A-like protein

B: Beta-lactamase class A-like protein

C: Beta-lactamase class A-like protein

D: Beta-lactamase class A-like protein

E: Beta-lactamase class A-like protein

hetero molecules

161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase class A-like protein

B: Beta-lactamase class A-like protein

hetero molecules

defined by author&software
64.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Beta-lactamase class A-like protein

D: Beta-lactamase class A-like protein

hetero molecules

defined by author&software
64.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Beta-lactamase class A-like protein

hetero molecules

E: Beta-lactamase class A-like protein

hetero molecules

defined by author&software
65 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	117.398, 163.106, 113.009
Angle α, β, γ (deg.)	90.000, 90.380, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	E-307- NA
2	1	E-670- HOH
3	1	E-679- HOH

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. Possible dimer as observed in the crystal, A + B, C+D, and E (x,y,z) + E (-x,y, 2-z)

#1: Protein	Beta-lactamase class A-like protein Mass: 31888.445 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0488 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1BLB4
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1497 / 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: 3.39 Å³/Da / Density % sol: 63.75 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES:NaOH pH 7.5, 10% PEG 4000, 5% propanol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97926, 0.97942

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 14, 2011

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	0.97926	1
2	0.97942	1

Reflection

Redundancy: 4.6 % / Av σ(I) over netI: 20.12 / Number: 751902 / R_merge(I) obs: 0.102 / Χ²: 1.92 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 162703 / % possible obs: 97.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.16	50	98.3	1	0.086	6.089	4.6
4.09	5.16	99.6	1	0.066	3.841	4.7
3.58	4.09	99.6	1	0.065	3.158	4.7
3.25	3.58	99.5	1	0.075	2.853	4.8
3.02	3.25	99.4	1	0.089	2.431	4.8
2.84	3.02	99.4	1	0.101	1.963	4.8
2.7	2.84	99.2	1	0.107	1.771	4.8
2.58	2.7	99	1	0.117	1.628	4.8
2.48	2.58	98.9	1	0.131	1.491	4.8
2.39	2.48	98.9	1	0.147	1.536	4.8
2.32	2.39	98.8	1	0.16	1.307	4.8
2.25	2.32	98.7	1	0.16	1.237	4.7
2.19	2.25	98.4	1	0.17	1.229	4.7
2.14	2.19	98.6	1	0.191	1.135	4.7
2.09	2.14	98.5	1	0.21	1.056	4.7
2.05	2.09	98.2	1	0.247	1.017	4.6
2.01	2.05	97.9	1	0.281	0.989	4.6
1.97	2.01	97	1	0.31	0.95	4.3
1.93	1.97	96	1	0.348	0.921	4
1.9	1.93	78.5	1	0.432	0.905	3.6

Reflection

Resolution: 1.9→50 Å / Num. all: 162703 / Num. obs: 162703 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 18.7 Å² / R_merge(I) obs: 0.102 / Χ²: 1.917 / Net I/σ(I): 7.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9-1.93	3.6	0.432	6529	0.905	1	78.5
1.93-1.97	4	0.348	7980	0.921	1	96
1.97-2.01	4.3	0.31	8034	0.95	1	97
2.01-2.05	4.6	0.281	8159	0.989	1	97.9
2.05-2.09	4.6	0.247	8183	1.017	1	98.2
2.09-2.14	4.7	0.21	8172	1.056	1	98.5
2.14-2.19	4.7	0.191	8182	1.135	1	98.6
2.19-2.25	4.7	0.17	8190	1.229	1	98.4
2.25-2.32	4.7	0.16	8189	1.237	1	98.7
2.32-2.39	4.8	0.16	8261	1.307	1	98.8
2.39-2.48	4.8	0.147	8199	1.536	1	98.9
2.48-2.58	4.8	0.131	8259	1.491	1	98.9
2.58-2.7	4.8	0.117	8220	1.628	1	99
2.7-2.84	4.8	0.107	8243	1.771	1	99.2
2.84-3.02	4.8	0.101	8323	1.963	1	99.4
3.02-3.25	4.8	0.089	8295	2.431	1	99.4
3.25-3.58	4.8	0.075	8291	2.853	1	99.5
3.58-4.09	4.7	0.065	8314	3.158	1	99.6
4.09-5.16	4.7	0.066	8347	3.841	1	99.6
5.16-50	4.6	0.086	8333	6.089	1	98.3

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2 Å / D res low: 50 Å / FOM : 0.424 / FOM acentric: 0.427 / FOM centric: 0.271 / Reflection: 141260 / Reflection acentric: 138948 / Reflection centric: 2312

Phasing MAD set

Highest resolution: 2 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	1.88	1	0.8	0.4	0	0	138948	2312
2	0.93	0.89	37.6	50.8	0.65	0.48	120213	2101

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	12.5-50	2.61	1	2.2	0.8	0	0	462	38
1	7.14-12.5	1.68	1	1.6	0.8	0	0	2450	120
1	5-7.14	1.98	1	1.5	0.7	0	0	5852	204
1	3.85-5	1.22	1	1.2	0.8	0	0	10693	270
1	3.13-3.85	1.33	1	1	0.7	0	0	16972	327
1	2.63-3.13	1.97	1	0.8	0.4	0	0	24676	401
1	2.27-2.63	2.46	1	0.7	0.2	0	0	33748	442
1	2-2.27	2.72	1	0.5	0.2	0	0	44095	510
2	12.5-50	0.94	0.88	36.6	54	1.64	0.99	461	38
2	7.14-12.5	0.78	0.72	33.2	43.5	1.54	1.06	2450	120
2	5-7.14	0.8	0.75	36.5	44.4	1.27	0.87	5849	204
2	3.85-5	0.89	0.83	46.8	58.1	0.81	0.59	10692	270
2	3.13-3.85	0.9	0.89	43.9	58.5	0.73	0.48	16966	327
2	2.63-3.13	0.93	0.94	36.2	52.4	0.65	0.37	24649	401
2	2.27-2.63	0.96	0.97	34.2	46	0.54	0.32	33647	442
2	2-2.27	0.98	0.98	36.2	47.6	0.4	0.23	25499	299

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	25.0317	-0.715	-0.024	-0.099	3.481	0
2	22.4249	-0.559	0.118	0.102	3.37	0
3	24.3807	-0.677	0.054	-0.304	3.4	0
4	24.339	-0.728	-0.126	-0.476	3.313	0
5	24.6286	-0.669	-0.128	-0.503	3.416	0
6	24.8974	-0.693	0.096	-0.278	3.147	0
7	22.4135	-0.574	-0.177	-0.297	3.238	0
8	25.5425	-0.776	-0.059	-0.189	3.167	0
9	23.4963	-0.506	0.121	0.181	3.157	0
10	30.6165	-0.622	0.15	0.012	3.141	0
11	27.3766	-0.548	-0.23	-0.385	3.024	0
12	28.5099	-0.608	0.142	0.074	2.957	0
13	35.5795	-0.699	0.019	-0.383	3.249	0
14	28.8011	-0.628	-0.153	-0.581	3.378	0
15	24.7414	-0.761	-0.051	-0.127	2.919	0
16	26.6718	-0.553	-0.217	-0.323	3.12	0
17	32.5149	-0.637	0.126	-0.328	2.968	0
18	34.8882	-0.704	0.013	-0.021	3.184	0
19	35.6157	-0.743	-0.099	-0.075	3.046	0
20	27.4909	-0.7	0.108	-0.216	3.125	0
21	26.4036	-0.747	-0.126	-0.414	3.013	0
22	27.6573	-0.619	-0.156	-0.219	3.258	0
23	28.6896	-0.682	-0.289	-0.318	2.544	0
24	37.6783	-0.666	0.114	0.124	2.926	0
25	26.2789	-0.783	-0.237	-0.48	2.673	0
26	36.3441	-0.483	-0.219	-0.272	3.031	0
27	36.8539	-0.753	-0.079	-0.528	2.885	0
28	25.7241	-0.896	0.016	-0.126	2.39	0
29	26.0399	-0.564	0.231	0.224	2.44	0
30	30.1083	-0.661	-0.269	-0.173	2.527	0
31	71.8931	-0.731	0.088	-0.381	2.54	0
32	43.7459	-0.79	-0.026	-0.023	2.509	0
33	27.2195	-0.562	0.255	0.079	2.238	0
34	32.7642	-0.73	-0.158	-0.58	2.831	0
35	29.7574	-0.823	0.094	-0.429	2.33	0
36	37.7169	-0.867	0.008	0.02	2.444	0
37	31.0697	-0.764	-0.218	-0.625	2.167	0
38	22.8746	-0.634	-0.158	-0.54	2.191	0
39	24.66	-0.856	0.101	-0.285	2.354	0
40	30.0078	-0.707	0.022	-0.342	2.221	0
41	64.4386	-0.593	-0.227	-0.219	2.341	0
42	35.9394	-0.712	0.014	-0.062	2.06	0
43	23.5675	-0.624	-0.162	-0.26	2.062	0
44	45.843	-0.642	0.098	0.078	2.269	0
45	21.0688	-0.663	-0.16	-0.516	1.856	0
46	40.7253	-0.624	0.104	-0.28	2.128	0
47	24.9009	-0.717	0.041	-0.317	1.852	0
48	19.709	-0.507	0.128	0.14	1.908	0
49	35.3137	-0.49	-0.196	-0.319	2.056	0
50	37.6397	-0.72	-0.076	-0.481	2.25	0
51	34.5776	-0.714	-0.088	-0.121	2.132	0
52	44.2985	-0.587	0.166	0.177	2.414	0
53	24.7175	-0.736	0.004	-0.087	1.685	0
54	22.2345	-0.528	0.141	0.115	1.762	0
55	25.536	-0.733	-0.262	-0.544	1.348	0
56	25.8622	-0.617	-0.182	-0.284	1.719	0
57	27.1462	-0.503	0.255	0.146	1.104	0
58	32.2758	-0.874	0.06	-0.35	1.305	0
59	33.7098	-0.73	-0.263	-0.254	1.288	0
60	25.7087	-0.878	0.057	-0.06	1.124	0
61	51.0511	-0.781	-0.292	-0.71	1.119	0
62	47.348	-0.645	-0.014	-0.141	0.268	0
63	15.6533	-0.715	-0.025	-0.099	2.405	-0.098
64	16.3557	-0.558	0.118	0.102	2.404	-0.091
65	20.2031	-0.677	0.054	-0.304	2.464	-0.093
66	16.6789	-0.728	-0.126	-0.476	1.992	-0.107
67	20.7025	-0.669	-0.128	-0.503	2.427	-0.091
68	20.5803	-0.693	0.095	-0.278	1.993	-0.123
69	18.6246	-0.574	-0.177	-0.297	2.418	-0.102
70	19.9623	-0.776	-0.059	-0.189	1.858	-0.107
71	23.4054	-0.506	0.121	0.181	2.059	-0.139
72	23.7066	-0.622	0.15	0.012	1.847	-0.101
73	19.1113	-0.548	-0.23	-0.385	1.762	-0.101
74	24.8297	-0.608	0.142	0.074	1.85	-0.116
75	30.0994	-0.699	0.018	-0.383	2.036	-0.129
76	29.5642	-0.628	-0.153	-0.581	2.194	-0.14
77	18.995	-0.762	-0.052	-0.127	1.833	-0.106
78	23.7736	-0.553	-0.217	-0.323	1.89	-0.12
79	35.1664	-0.637	0.125	-0.328	2.017	-0.116
80	34.5076	-0.704	0.013	-0.021	2.019	-0.131
81	27.7337	-0.743	-0.1	-0.075	1.839	-0.107
82	17.1819	-0.7	0.108	-0.216	1.838	-0.101
83	26.8571	-0.746	-0.127	-0.414	1.918	-0.114
84	19.8357	-0.619	-0.156	-0.219	2.147	-0.127
85	22.9164	-0.682	-0.29	-0.318	1.849	-0.065
86	26.5077	-0.666	0.113	0.124	1.867	-0.105
87	17.8716	-0.783	-0.237	-0.48	1.888	-0.063
88	32.562	-0.483	-0.219	-0.272	1.851	-0.12
89	29.2782	-0.752	-0.08	-0.528	1.754	-0.099
90	17.6772	-0.897	0.015	-0.126	1.627	-0.05
91	19.9229	-0.565	0.231	0.225	1.411	-0.09
92	33.6103	-0.662	-0.269	-0.173	1.532	-0.094
93	62.2524	-0.733	0.088	-0.382	1.64	-0.081
94	44.5159	-0.791	-0.026	-0.023	1.606	-0.084
95	21.1922	-0.563	0.255	0.079	1.466	-0.053
96	30.871	-0.731	-0.158	-0.58	1.821	-0.086
97	20.3146	-0.823	0.094	-0.43	1.33	-0.076
98	39.3139	-0.866	0.007	0.021	1.412	-0.103
99	31.0787	-0.765	-0.218	-0.626	1.282	-0.098
100	18.3017	-0.634	-0.158	-0.54	1.385	-0.082
101	22.8448	-0.856	0.101	-0.285	1.754	-0.065
102	46.9181	-0.707	0.022	-0.342	1.615	-0.101
103	52.8417	-0.593	-0.228	-0.219	1.602	-0.065
104	43.8415	-0.711	0.014	-0.062	1.451	-0.08
105	21.3544	-0.624	-0.162	-0.26	1.358	-0.084
106	35.532	-0.642	0.098	0.078	1.295	-0.092
107	11.3872	-0.663	-0.16	-0.516	1.233	-0.048
108	31.5892	-0.624	0.104	-0.28	1.319	-0.098
109	24.5949	-0.718	0.041	-0.317	1.319	-0.05
110	18.5695	-0.507	0.127	0.14	1.226	-0.072
111	34.4145	-0.489	-0.197	-0.319	1.133	-0.074
112	43.736	-0.72	-0.076	-0.48	1.366	-0.095
113	33.6399	-0.714	-0.09	-0.121	1.333	-0.093
114	41.7328	-0.587	0.167	0.178	1.502	-0.086
115	25.5721	-0.735	0.003	-0.087	1.233	-0.049
116	25.0458	-0.528	0.141	0.115	1.286	-0.054
117	23.8518	-0.734	-0.263	-0.544	0.818	-0.037
118	35.2372	-0.617	-0.182	-0.285	1.252	-0.044
119	19.6209	-0.502	0.255	0.145	0.804	-0.045
120	29.5551	-0.874	0.06	-0.35	0.96	-0.047
121	33.0731	-0.73	-0.263	-0.254	0.953	-0.043
122	25.7737	-0.878	0.057	-0.061	0.767	-0.037
123	34.7675	-0.782	-0.293	-0.709	0.572	-0.039
124	22.687	-0.641	-0.012	-0.142	0.188	-0.006

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.5-50	0.691	0.707	0.5	500	462	38
7.14-12.5	0.739	0.747	0.582	2570	2450	120
5-7.14	0.717	0.725	0.489	6056	5852	204
3.85-5	0.633	0.638	0.405	10963	10693	270
3.13-3.85	0.59	0.595	0.353	17299	16972	327
2.63-3.13	0.488	0.492	0.259	25077	24676	401
2.27-2.63	0.383	0.386	0.169	34190	33748	442
2-2.27	0.244	0.246	0.067	44605	44095	510

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 162638

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.3-100	51.3	0.864	969
7.28-10.3	43.2	0.925	1929
5.95-7.28	41.5	0.919	2497
5.15-5.95	40.2	0.933	2957
4.61-5.15	41.8	0.933	3331
4.2-4.61	45.7	0.94	3667
3.89-4.2	45.6	0.933	4008
3.64-3.89	45.2	0.931	4308
3.43-3.64	45.8	0.925	4551
3.26-3.43	47.1	0.925	4813
3.11-3.26	49.7	0.919	5084
2.97-3.11	49.8	0.913	5273
2.86-2.97	51.9	0.905	5501
2.75-2.86	52.1	0.914	5741
2.66-2.75	53.7	0.921	5905
2.57-2.66	53.4	0.921	6089
2.5-2.57	54.4	0.921	6334
2.43-2.5	55.7	0.921	6495
2.36-2.43	57.6	0.925	6631
2.3-2.36	59.3	0.923	6835
2.25-2.3	61.2	0.927	7017
2.2-2.25	62.2	0.927	7140
2.15-2.2	64	0.925	7310
2.1-2.15	66.1	0.921	7442
2.06-2.1	70.7	0.92	7621
2.02-2.06	71.5	0.91	7749
1.98-2.02	81.3	0.904	7843
1.95-1.98	90.9	0.87	7930
1.9-1.95	90	0.729	9668

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	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
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.9→33.49 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.962 / WR_factor R_free: 0.1491 / WR_factor R_work: 0.1293 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9356 / SU B: 3.605 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0927 / SU R_free: 0.0887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.089
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	0.1596	8180	5 %	RANDOM
R_work	0.1369	-	-	-
all	0.1381	162606	-	-
obs	0.1381	162606	97.91 %	-

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: 79.47 Å² / B_iso mean: 23.2372 Å² / B_iso min: 10.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.91 Å²	0 Å²	1.36 Å²
2-	-	-0.63 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→33.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10746	0	120	1497	12363

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	11245
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10821
X-RAY DIFFRACTION	r_angle_refined_deg	1.593	1.984	15165
X-RAY DIFFRACTION	r_angle_other_deg	0.828	3	24832
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.651	5	1401
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.63	23.896	557
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.442	15	1832
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.907	15	97
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1695
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12829
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2620

LS refinement shell

Resolution: 1.903→1.952 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.236	552	-
R_work	0.213	10358	-
all	-	10910	-
obs	-	-	89.5 %

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	0.734	0.2634	0.0091	1.0333	0.2022	1.1377	-0.0164	0.0661	-0.0752	-0.0841	0.0103	0.1592	0.1367	-0.1307	0.0061	0.0589	-0.0427	-0.0504	0.1082	-0.0339	0.1219	26.4667	120.1238	45.6297
2	0.5017	-0.1338	0.0422	0.4286	0.1859	1.2104	-0.0047	0.0521	0.0477	-0.0341	-0.0239	0.0532	-0.128	-0.0344	0.0286	0.0293	0.0034	-0.0301	0.0168	0.005	0.0556	39.1492	145.4053	55.7665
3	2.9076	2.0863	-0.5018	5.3444	-0.7607	24.1872	0.2953	-0.1765	-0.0696	0.0204	-0.2877	0.3454	0.2735	-0.4632	-0.0076	0.059	0.0229	-0.033	0.1276	-0.0323	0.0674	20.3451	148.3762	60.1281
4	0.4929	0.1391	0.0092	0.7343	-0.1166	0.6698	0.0034	0.0245	-0.0393	-0.0059	-0.0002	0.0508	0.0632	-0.079	-0.0032	0.0262	-0.0135	-0.0265	0.05	-0.0265	0.069	35.7179	126.1219	53.0082
5	3.0812	1.9061	0.9768	10.3765	9.5669	21.7212	0.0964	-0.4391	-0.0864	0.3228	-0.1162	-0.2049	0.0463	-0.0854	0.0198	0.0744	-0.0342	0.0005	0.1067	0.0395	0.0562	25.6809	116.3163	99.0462
6	0.6471	0.34	-0.0945	1.294	0.2075	1.0257	-0.0231	-0.0288	-0.1701	0.0719	-0.0138	0.05	0.1635	-0.0387	0.037	0.0898	-0.0203	0.0065	0.0141	0.0236	0.0876	34.7121	116.0501	87.4974
7	0.5475	-0.1054	-0.1018	0.5309	-0.1796	1.1753	-0.0322	-0.0474	-0.0218	0.0561	-0.005	-0.05	-0.0391	0.1007	0.0372	0.0193	-0.0016	-0.0263	0.0286	0.0029	0.0479	52.3676	136.0972	79.8441
8	0.5779	0.2557	0.0767	0.4985	-0.0956	0.6181	-0.0144	0.011	-0.0546	0.0333	0.0051	0.033	0.0789	-0.0294	0.0093	0.0264	-0.0079	0.0028	0.0085	0.0098	0.0461	36.5605	126.1781	82.3297
9	2.0724	0.0566	0.4115	1.0032	-0.5409	1.4287	0.0102	-0.1919	0.0953	0.1487	0.0928	0.3372	-0.0787	-0.3854	-0.103	0.0304	0.0077	0.0676	0.227	0.0216	0.1626	10.1945	168.4226	109.9301
10	0.3201	0.0914	-0.2037	0.8151	0.013	1.3673	0.0059	-0.0555	-0.0634	0.0665	-0.0318	0.0188	0.1236	0.0033	0.0259	0.0248	-0.0082	-0.013	0.0195	0.0126	0.0391	35.1851	156.7306	102.1236
11	0.922	0.1509	-0.1961	0.805	-0.0522	1.0487	0.006	-0.0946	0.012	0.0936	-0.0108	0.0662	0.0074	-0.1303	0.0048	0.0167	-0.0101	0.0145	0.0453	-0.0086	0.0464	26.2935	166.3006	106.5479
12	1.233	0.0683	0.4983	1.248	-0.1174	1.7695	0.0077	-0.0365	0.0824	0.0567	0.0852	0.1636	-0.1341	-0.286	-0.0929	0.0172	0.0139	0.0294	0.1109	0.0083	0.1031	16.134	171.715	102.5096
13	1.3166	-0.8422	-0.4634	1.0505	0.1136	1.8576	0.0431	0.111	-0.0119	-0.1451	-0.0569	0.3101	-0.0783	-0.3332	0.0139	0.0815	0.0514	-0.0788	0.142	0.0135	0.2008	13.8047	178.074	69.5181
14	0.2286	0.0173	0.2284	0.738	-0.0865	1.2173	0.0106	0.0254	0.0342	-0.0675	-0.0356	-0.0377	-0.0338	0.1042	0.025	0.0162	0.0012	-0.0075	0.0257	0.0082	0.0383	40.6532	172.2574	78.2838
15	0.1297	-0.3976	-0.0271	2.8872	0.5224	0.8936	0.0131	0.033	-0.0029	-0.0658	0.0004	-0.0052	-0.0577	0.0328	-0.0135	0.0393	0.0105	-0.0321	0.0266	0.0036	0.0535	31.6891	173.7567	70.7878
16	1.0756	-0.2673	-0.2922	0.8998	0.0321	1.24	0.0004	-0.0262	-0.0625	-0.0257	0.0338	0.2271	0.022	-0.2226	-0.0342	0.0263	0.0017	-0.0418	0.0623	0.0133	0.1088	18.0495	170.1971	77.7938
17	0.7888	0.2632	0.1125	1.6725	0.3183	1.6154	-0.036	0.0901	0.2448	-0.1046	0.0367	0.0808	-0.2521	-0.0168	-0.0007	0.0871	-0.0294	-0.0117	0.0453	0.0541	0.1082	4.5426	125.2042	92.7205
18	0.6619	0.061	-0.039	0.3148	-0.223	0.9877	-0.043	0.0489	-0.0369	-0.0196	0.006	-0.0432	0.0978	0.0678	0.037	0.0195	0.0022	-0.0072	0.0328	-0.0058	0.0294	8.0083	98.0538	101.3349
19	0.6808	0.0982	-0.0406	0.6779	-0.1964	0.5548	-0.0451	0.0809	0.0549	-0.0489	0.0337	0.0537	-0.0135	0.0114	0.0114	0.0124	-0.0145	-0.0185	0.0375	0.0203	0.0304	0.7828	109.1195	96.2154
20	1.0565	0.0267	0.2094	1.1859	0.3851	1.4089	0.0343	0.0304	0.1419	-0.0048	-0.0003	0.1275	-0.1787	-0.0606	-0.034	0.043	-0.0074	-0.0054	0.0349	0.0339	0.0843	-0.734	120.6373	100.1138

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 53
2	X-RAY DIFFRACTION	2	A	54 - 154
3	X-RAY DIFFRACTION	3	A	155 - 162
4	X-RAY DIFFRACTION	4	A	163 - 272
5	X-RAY DIFFRACTION	5	B	-2 - 9
6	X-RAY DIFFRACTION	6	B	10 - 55
7	X-RAY DIFFRACTION	7	B	56 - 154
8	X-RAY DIFFRACTION	8	B	155 - 272
9	X-RAY DIFFRACTION	9	C	5 - 55
10	X-RAY DIFFRACTION	10	C	56 - 156
11	X-RAY DIFFRACTION	11	C	157 - 209
12	X-RAY DIFFRACTION	12	C	210 - 272
13	X-RAY DIFFRACTION	13	D	5 - 54
14	X-RAY DIFFRACTION	14	D	55 - 154
15	X-RAY DIFFRACTION	15	D	155 - 190
16	X-RAY DIFFRACTION	16	D	191 - 272
17	X-RAY DIFFRACTION	17	E	5 - 54
18	X-RAY DIFFRACTION	18	E	55 - 158
19	X-RAY DIFFRACTION	19	E	159 - 209
20	X-RAY DIFFRACTION	20	E	210 - 272

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