PDB-2goy: Crystal structure of assimilatory adenosine 5'-phosphosulfate red...

ID or keywords:

Entry

Database: PDB / ID: 2goy

Title

Crystal structure of assimilatory adenosine 5'-phosphosulfate reductase with bound APS

Components

adenosine phosphosulfate reductase

Keywords

OXIDOREDUCTASE / Iron sulfur cluster / nucleotide binding / adenosine 5'-phosphosulfate / thiosulfonate intermediate

Function / homology

Function and homology information

adenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate reductase (thioredoxin) activity / phosphoadenylyl-sulfate reductase (thioredoxin) activity / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Chartron, J. / Carroll, K.S. / Shiau, C. / Gao, H. / Leary, J.A. / Bertozzi, C.R. / Stout, C.D.

Citation

Journal: J.Mol.Biol. / Year: 2006
Title: Substrate Recognition, Protein Dynamics, and Iron-Sulfur Cluster in Pseudomonas aeruginosa Adenosine 5'-Phosphosulfate Reductase.
Authors: Chartron, J. / Carroll, K.S. / Shiau, C. / Gao, H. / Leary, J.A. / Bertozzi, C.R. / Stout, C.D.

History

Deposition	Apr 14, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE Roughly 50% of the protein in the preparation is missing the first three amino acids from ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2goy.cif.gz	375.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2goy.ent.gz	301.9 KB	Display	PDB format
PDBx/mmJSON format	2goy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	1jnr 1sur
Similar structure data	5mho-1 5ms8-1 3juj-d 4kty-2 2z1b-d 5mho-2 4d9p-3 4gb1-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: adenosine phosphosulfate reductase

B: adenosine phosphosulfate reductase

C: adenosine phosphosulfate reductase

D: adenosine phosphosulfate reductase

E: adenosine phosphosulfate reductase

F: adenosine phosphosulfate reductase

G: adenosine phosphosulfate reductase

H: adenosine phosphosulfate reductase

hetero molecules

255 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: adenosine phosphosulfate reductase

B: adenosine phosphosulfate reductase

C: adenosine phosphosulfate reductase

D: adenosine phosphosulfate reductase

hetero molecules

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

2

E: adenosine phosphosulfate reductase

F: adenosine phosphosulfate reductase

G: adenosine phosphosulfate reductase

H: adenosine phosphosulfate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.027, 102.788, 139.374
Angle α, β, γ (deg.)	90.10, 102.57, 89.95
Int Tables number	1
Space group name H-M	P1

Details

The biological assembly consists of a tetramer of polypeptides. Two such tetramers are present in the asymmetric unit and are related by a pseudo 2(1) screw axis.

#1: Protein	adenosine phosphosulfate reductase / APS reductase / thioredoxin dependent / AdoPS reductase / APS sulfotransferase Mass: 31326.457 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cysH / Plasmid: pET24b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O05927, adenylyl-sulfate reductase (thioredoxin)
#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₁₀PS
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.35 Å³/Da / Density % sol: 63.25 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 1.5M ammonium sulfate, 0.1M sodium cacodylate, 2.5mM APS, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	123	1
2	123	1
3	123	1
4		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL9-1	1	0.98397
SYNCHROTRON	SSRL	BL9-2	2	1.73108
SYNCHROTRON	SSRL	BL9-2	3	1.73710, 1.74203, 1.73710

Detector

Type	ID	Detector	Date
MAR scanner 345 mm plate	1	IMAGE PLATE	Mar 5, 2005
ADSC QUANTUM 315	2	CCD	Mar 6, 2005
MARMOSAIC 325 mm CCD	3	CCD	Apr 1, 2005

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degs.	SINGLE WAVELENGTH	M	x-ray	1
2	Double Crystal	SINGLE WAVELENGTH	M	x-ray	1
3	Double Crystal	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.98397	1
2	1.73108	1
3	1.7371	1
4	1.74203	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	Num. obs	% possible obs
4.4	1	3.6	345284	0.173	0.173	2.792	29.683	79221	98.1
4.1	2	3.6	311854	0.165	0.165	2.795	68.359	76858	95
4.3	3	2.8	473117	0.207	0.207	2.483	29.683	111236	97.9
6.3	4	4.5	391272	0.129	0.129	3.004	68.519	61646	94

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
8.85	136.08	2490	97.2	1	0.077	0.077	3.9
6.26	8.85	4647	99.4	1	0.084	0.084	4.2
5.11	6.26	5981	99.3	1	0.106	0.106	4.3
4.43	5.11	7088	98.8	1	0.108	0.108	4.3
3.96	4.43	7991	98.5	1	0.127	0.127	4.4
3.61	3.96	8859	98.6	1	0.2	0.2	4.4
3.35	3.61	9581	98.6	1	0.252	0.252	4.5
3.13	3.35	10252	97.2	1	0.325	0.325	4.4
2.95	3.13	10868	97.3	1	0.503	0.503	4.4
2.8	2.95	11464	97.2	1	0.767	0.767	4.4
8.85	136.08	2496	97.4	2	0.069	0.069	3.8
6.26	8.85	4541	97.1	2	0.075	0.075	3.9
5.11	6.26	5856	96.9	2	0.095	0.095	4
4.43	5.11	6893	96.1	2	0.1	0.1	4
3.96	4.43	7774	95.8	2	0.116	0.116	4
3.61	3.96	8587	95.4	2	0.189	0.189	4.1
3.35	3.61	9250	95.3	2	0.23	0.23	4.1
3.13	3.35	9927	93.9	2	0.299	0.299	4.1
2.95	3.13	10502	93.7	2	0.459	0.459	4.1
2.8	2.95	11032	93.4	2	0.674	0.674	4.1
7.91	137.36	3504	97.6	3	0.091	0.091	4
5.59	7.91	6542	99.3	3	0.111	0.111	4.1
4.56	5.59	8408	99	3	0.131	0.131	4.2
3.95	4.56	9962	98.8	3	0.15	0.15	4.2
3.54	3.95	11261	98.7	3	0.221	0.221	4.3
3.23	3.54	12412	98.2	3	0.244	0.244	4.4
2.99	3.23	13427	97.8	3	0.307	0.307	4.4
2.8	2.99	14468	97.6	3	0.399	0.399	4.3
2.64	2.8	15259	97.3	3	0.54	0.54	4.2
2.5	2.64	15993	96.2	3	0.717	0.717	4.1
13.42	68.52	734	99	4	0.071	0.071	7.7
9.49	13.42	1348	99.3	4	0.07	0.07	7.8
7.75	9.49	1726	99.2	4	0.075	0.075	7.8
6.71	7.75	1971	96.1	4	0.088	0.088	7.8
6	6.71	2017	85.6	4	0.102	0.102	7.6
5.48	6	2349	90.8	4	0.117	0.117	7.7
5.07	5.48	2663	93.2	4	0.108	0.108	7.7
4.74	5.07	2866	94.4	4	0.112	0.112	7.8
4.47	4.74	3040	93.7	4	0.111	0.111	7.7
4.24	4.47	3207	94.3	4	0.118	0.118	7.7
4.05	4.24	3402	95	4	0.129	0.129	7.7
3.87	4.05	3560	94.6	4	0.152	0.152	7.8
3.72	3.87	3724	95.2	4	0.162	0.162	7.7
3.59	3.72	3875	94.7	4	0.183	0.183	7.8
3.46	3.59	4030	94.9	4	0.183	0.183	6.6
3.35	3.46	4040	94.4	4	0.151	0.151	3.9
3.25	3.35	4341	94.4	4	0.161	0.161	3.9
3.16	3.25	4313	94.5	4	0.202	0.202	3.9
3.08	3.16	4574	94.5	4	0.234	0.234	3.9
3.01	3.08	3866	89	4	0.272	0.272	3.9

Reflection

Resolution: 2.7→38.674 Å / Num. all: 85404 / Num. obs: 85404 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / R_merge(I) obs: 0.105 / R_sym value: 0.105 / Net I/σ(I): 5.9

Reflection shell

Redundancy: 2 %

Resolution (Å)	% possible obs (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_sym value
2.7-2.77	95.7	0.337	1.9	12387	6341	0.337
2.77-2.85	95.9	0.279	2.3	12113	6199	0.279
2.85-2.93	95.8	0.231	2.8	11672	5947	0.231
2.93-3.02	96.4	0.209	3.1	11567	5903	0.209
3.02-3.12	96.2	0.178	3.7	11102	5644	0.178
3.12-3.23	96	0.158	4	10839	5499	0.158
3.23-3.35	96.2	0.12	5	10470	5300	0.12
3.35-3.49	96.2	0.102	6.2	10006	5072	0.102
3.49-3.64	95.9	0.08	8.3	9579	4854	0.08
3.64-3.82	95.8	0.072	9	9165	4642	0.072
3.82-4.02	96.1	0.068	6.4	8842	4478	0.068
4.02-4.27	95.6	0.053	12.1	8246	4180	0.053
4.27-4.56	95.5	0.049	13.3	7725	3914	0.049
4.56-4.93	94.9	0.047	14.6	7144	3627	0.047
4.93-5.4	95	0.055	11.1	6618	3354	0.055
5.4-6.04	93.7	0.057	11.2	5826	2957	0.057
6.04-6.97	91.7	0.049	13.9	5033	2550	0.049
6.97-8.54	92	0.039	17.7	4291	2183	0.039
8.54-12.07	99	0.028	18.2	3568	1807	0.028
12.07-38.67	96.2	0.02	36.4	1868	953	0.02

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 3.49 Å / D res low: 29.65 Å / FOM : 0.53 / FOM acentric: 0.53 / FOM centric: 0 / Reflection: 77916

Phasing MAD set

R cullis centric: 0 / R kraut centric: 0 / Highest resolution: 3.49 Å / Lowest resolution: 29.65 Å / FOM centric: 0 / Loc centric: 0 / Power centric: 0

ID	R cullis	R cullis acentric	R kraut	R kraut acentric	FOM	FOM acentric	Loc	Loc acentric	Power (kW)	Power acentric
f_rem_FRIED	0.989	0.989	0.064	0.064	0.114	0.114	40.298	40.298	0.383	0.383
f_peak	0.81	0.81	0.093	0.093	0.285	0.285	55.012	55.012	1.214	1.214
f_peak_FRIED	0.784	0.784	0.097	0.097	0.307	0.307	56.293	56.293	1.304	1.304
f_infl	0.759	0.759	0.094	0.094	0.32	0.32	54.025	54.025	1.44	1.44
f_infl_FRIED	0.738	0.738	0.094	0.094	0.333	0.333	53.34	53.34	1.527	1.527

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	Atom type	F double prime refined	F prime refined
3 wavelength	1	1	1.7371	FE	1.58	-0.29
3 wavelength	1	2	1.74203	FE	6.44	-12.61
3 wavelength	1	3	1.7371	FE	6.36	-14.34

Phasing MAD set shell

R cullis centric: 0 / R kraut centric: 0 / FOM centric: 0 / Loc centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis	R cullis acentric	R kraut	R kraut acentric	FOM	FOM acentric	Loc	Loc acentric	Power (kW)	Power acentric
f_rem_FRIED	6.95-29.65	0.814	0.814	0.036	0.036	0.259	0.259	29.284	29.284	0.939	0.939
f_rem_FRIED	5.53-6.95	0.913	0.913	0.046	0.046	0.199	0.199	27.645	27.645	0.727	0.727
f_rem_FRIED	4.84-5.53	0.967	0.967	0.054	0.054	0.128	0.128	34.21	34.21	0.454	0.454
f_rem_FRIED	4.39-4.84	1.007	1.007	0.059	0.059	0.084	0.084	41.037	41.037	0.303	0.303
f_rem_FRIED	4.08-4.39	0.997	0.997	0.065	0.065	0.071	0.071	43.151	43.151	0.25	0.25
f_rem_FRIED	3.84-4.08	1.027	1.027	0.078	0.078	0.056	0.056	45.489	45.489	0.218	0.218
f_rem_FRIED	3.65-3.84	1.024	1.024	0.091	0.091	0.049	0.049	53.108	53.108	0.182	0.182
f_rem_FRIED	3.49-3.65	1.034	1.034	0.104	0.104	0.047	0.047	50.855	50.855	0.195	0.195
f_peak	6.95-29.65	0.549	0.549	0.068	0.068	0.448	0.448	38.411	38.411	3.007	3.007
f_peak	5.53-6.95	0.66	0.66	0.089	0.089	0.406	0.406	38.876	38.876	2.247	2.247
f_peak	4.84-5.53	0.764	0.764	0.086	0.086	0.338	0.338	45.746	45.746	1.51	1.51
f_peak	4.39-4.84	0.812	0.812	0.082	0.082	0.269	0.269	55.429	55.429	1.005	1.005
f_peak	4.08-4.39	0.836	0.836	0.086	0.086	0.237	0.237	58.1	58.1	0.839	0.839
f_peak	3.84-4.08	0.897	0.897	0.102	0.102	0.198	0.198	62.433	62.433	0.718	0.718
f_peak	3.65-3.84	0.893	0.893	0.123	0.123	0.184	0.184	78.216	78.216	0.566	0.566
f_peak	3.49-3.65	0.91	0.91	0.126	0.126	0.177	0.177	65.636	65.636	0.689	0.689
f_peak_FRIED	6.95-29.65	0.495	0.495	0.067	0.067	0.473	0.473	37.876	37.876	3.361	3.361
f_peak_FRIED	5.53-6.95	0.612	0.612	0.09	0.09	0.435	0.435	38.349	38.349	2.512	2.512
f_peak_FRIED	4.84-5.53	0.725	0.725	0.09	0.09	0.368	0.368	45.884	45.884	1.661	1.661
f_peak_FRIED	4.39-4.84	0.791	0.791	0.087	0.087	0.294	0.294	56.622	56.622	1.085	1.085
f_peak_FRIED	4.08-4.39	0.814	0.814	0.09	0.09	0.261	0.261	60.031	60.031	0.896	0.896
f_peak_FRIED	3.84-4.08	0.881	0.881	0.109	0.109	0.216	0.216	64.982	64.982	0.761	0.761
f_peak_FRIED	3.65-3.84	0.876	0.876	0.127	0.127	0.2	0.2	79.411	79.411	0.615	0.615
f_peak_FRIED	3.49-3.65	0.901	0.901	0.135	0.135	0.188	0.188	70.307	70.307	0.709	0.709
f_infl	6.95-29.65	0.435	0.435	0.063	0.063	0.481	0.481	34.764	34.764	3.909	3.909
f_infl	5.53-6.95	0.579	0.579	0.09	0.09	0.444	0.444	37.094	37.094	2.739	2.739
f_infl	4.84-5.53	0.707	0.707	0.089	0.089	0.381	0.381	44.9	44.9	1.784	1.784
f_infl	4.39-4.84	0.774	0.774	0.084	0.084	0.31	0.31	54.951	54.951	1.177	1.177
f_infl	4.08-4.39	0.815	0.815	0.089	0.089	0.271	0.271	59.3	59.3	0.952	0.952
f_infl	3.84-4.08	0.863	0.863	0.106	0.106	0.232	0.232	62.048	62.048	0.838	0.838
f_infl	3.65-3.84	0.864	0.864	0.124	0.124	0.215	0.215	76.376	76.376	0.671	0.671
f_infl	3.49-3.65	0.894	0.894	0.131	0.131	0.2	0.2	66.165	66.165	0.791	0.791
f_infl_FRIED	6.95-29.65	0.417	0.417	0.062	0.062	0.493	0.493	34.892	34.892	4.071	4.071
f_infl_FRIED	5.53-6.95	0.549	0.549	0.089	0.089	0.46	0.46	36.282	36.282	2.93	2.93
f_infl_FRIED	4.84-5.53	0.684	0.684	0.09	0.09	0.398	0.398	44.567	44.567	1.88	1.88
f_infl_FRIED	4.39-4.84	0.763	0.763	0.084	0.084	0.325	0.325	54.577	54.577	1.24	1.24
f_infl_FRIED	4.08-4.39	0.806	0.806	0.09	0.09	0.282	0.282	58.683	58.683	1.006	1.006
f_infl_FRIED	3.84-4.08	0.853	0.853	0.106	0.106	0.244	0.244	61.573	61.573	0.883	0.883
f_infl_FRIED	3.65-3.84	0.849	0.849	0.123	0.123	0.228	0.228	75.143	75.143	0.714	0.714
f_infl_FRIED	3.49-3.65	0.873	0.873	0.13	0.13	0.214	0.214	64.246	64.246	0.853	0.853

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	28.879	59.761	16.497	FE	1	1
2	30.947	60.538	14.902	FE	1	1
3	30.378	57.887	15.116	FE	1	1
4	31.48	59.191	17.166	FE	4.68547	1
5	19.866	65.812	54.69	FE	2.12934	1
6	18.887	68.056	55.887	FE	1	1
7	17.492	65.733	56.11	FE	2.21821	1
8	17.576	67.023	53.779	FE	4.44261	1

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection
6.95-29.65	0.7122	0.7122	9974
5.53-6.95	0.6429	0.6429	9982
4.84-5.53	0.5669	0.5669	9886
4.39-4.84	0.5207	0.5207	9869
4.08-4.39	0.494	0.494	9860
3.84-4.08	0.4456	0.4456	9803
3.65-3.84	0.4424	0.4424	9518
3.49-3.65	0.3982	0.3982	9024

Phasing dm

Delta phi final: 4.51 / Delta phi initial: 31.37 / FOM : 0.845 / Mask type: RMS / Method: FLIP / Reflection: 131256

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
11.05-500.01	1.469	0.841	2656
8.77-11.05	4.316	0.962	2564
7.66-8.77	3.328	0.94	2678
6.96-7.66	3.562	0.916	2600
6.46-6.96	3.172	0.903	2650
6.08-6.46	4.254	0.927	2568
5.78-6.08	3.87	0.895	2692
5.53-5.78	4.48	0.907	2586
5.31-5.53	3.962	0.899	2676
5.13-5.31	4.396	0.892	2558
4.97-5.13	4.75	0.884	2522
4.83-4.97	3.932	0.892	2728
4.7-4.83	4.619	0.9	2650
4.59-4.7	3.787	0.88	2580
4.48-4.59	4.417	0.887	2750
4.39-4.48	5.147	0.908	2538
4.3-4.39	4.591	0.91	2542
4.22-4.3	3.872	0.868	2730
4.14-4.22	4.61	0.895	2584
4.07-4.14	5.133	0.877	2688
4.01-4.07	6.476	0.836	2560
3.94-4.01	5.387	0.806	2648
3.89-3.94	5.512	0.838	2696
3.83-3.89	5.456	0.869	2576
3.78-3.83	6.215	0.856	2530
3.73-3.78	5.976	0.746	2696
3.68-3.73	5.651	0.786	2610
3.64-3.68	4.354	0.876	2692
3.6-3.64	6.611	0.762	2576
3.56-3.6	6.464	0.783	2586
3.52-3.56	5.959	0.791	2626
3.48-3.52	5.169	0.773	2720
3.45-3.48	5.211	0.797	2616
3.41-3.45	4.946	0.787	2540
3.38-3.41	4.076	0.829	2738
3.35-3.38	3.986	0.846	2432
3.32-3.35	4.555	0.769	2714
3.29-3.32	4.046	0.786	2690
3.26-3.29	4.068	0.821	2678
3.23-3.26	3.716	0.855	2542
3.21-3.23	4.055	0.832	2646
3.18-3.21	3.793	0.845	2582
3.15-3.18	3.922	0.77	2562
3.13-3.15	3.71	0.8	2720
3.11-3.13	3.888	0.819	2590
3.08-3.11	4.15	0.802	2734
3.06-3.08	4.36	0.79	2600
3.04-3.06	3.91	0.831	2508
3.02-3.04	4.188	0.791	2716
3-3.02	4.376	0.779	2592

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
CNS		phasing
CNS		refinement
PDB_EXTRACT	1.701	data extraction
Blu-Ice		data collection
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.7→38.68 Å / R_factor R_free error: 0.004 / Data cutoff high absF: 704616.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.265	4181	4.9 %	RANDOM
R_work	0.23	-	-	-
all	0.232	85402	-	-
obs	0.232	85402	95.5 %	-

Solvent computation

Solvent model: FLAT MODEL / B_sol: 30.416 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso mean: 38.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-15.08 Å²	0 Å²	6.92 Å²
2-	-	2.38 Å²	-6.36 Å²
3-	-	-	12.69 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.43 Å	0.36 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.58 Å	0.51 Å

Refinement step

Cycle: LAST / Resolution: 2.7→38.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14404	0	172	151	14727

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.008
X-RAY DIFFRACTION	c_angle_deg	1.5
X-RAY DIFFRACTION	c_dihedral_angle_d	22.1
X-RAY DIFFRACTION	c_improper_angle_d	3.18
X-RAY DIFFRACTION	c_mcbond_it	1.9	1.5
X-RAY DIFFRACTION	c_mcangle_it	3.11	2
X-RAY DIFFRACTION	c_scbond_it	2.73	2
X-RAY DIFFRACTION	c_scangle_it	4.01	2.5

LS refinement shell

Resolution: 2.7→2.87 Å / R_factor R_free error: 0.015 / Total num. of bins used: 6

	R_factor	Num. reflection	% reflection
R_free	0.37	645	4.5 %
R_work	0.333	13594	-
obs	-	14239	95.8 %

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	protein_rep.param	protein.top
X-RAY DIFFRACTION	2	water_rep.param	water.top
X-RAY DIFFRACTION	3	fs4.param	fs4.top
X-RAY DIFFRACTION	4	adx.param	adx.top

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