PDB-3llv: The Crystal Structure of the NAD(P)-binding domain of an Exopolyp...

ID or keywords:

Entry

Database: PDB / ID: 3llv

Title

The Crystal Structure of the NAD(P)-binding domain of an Exopolyphosphatase-related protein from Archaeoglobus fulgidus to 1.7A

Components

Exopolyphosphatase-related protein

Keywords

NAD(P) binding protein / NAD(P)-binding / Rossmann / Exopolyphosphatase-related / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

potassium ion transport / nucleic acid binding
Similarity search - Function

Biological species

Archaeoglobus fulgidus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.7 Å

Authors

Stein, A.J. / Chang, C. / Weger, A. / Hendricks, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of the NAD(P)-binding domain of an Exopolyphosphatase-related protein from Archaeoglobus fulgidus to 1.7A
Authors: Stein, A.J. / Chang, C. / Weger, A. / Hendricks, R. / Clancy, S. / Joachimiak, A.

History

Deposition	Jan 29, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 9, 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_special_symmetry / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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	3llv.cif.gz	41.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3llv.ent.gz	29.6 KB	Display	PDB format
PDBx/mmJSON format	3llv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3llv_validation.pdf.gz	431.3 KB	Display	wwPDB validaton report
Full document	3llv_full_validation.pdf.gz	431.9 KB	Display
Data in XML	3llv_validation.xml.gz	8.6 KB	Display
Data in CIF	3llv_validation.cif.gz	10.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/3llv ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3llv	HTTPS FTP

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Related structure data

Similar structure data	1ryf-2 4xid-1 3nru-11 3v33-1 9ant-1 2ecd-d 4xic-2 4m92-d 1plo-d 5jlx-2 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
Other databases	TargetDB: APC62008.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#38 - Feb 2003 Potassium Channels similarity (3)

Deposited unit

A: Exopolyphosphatase-related protein

hetero molecules

15.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Exopolyphosphatase-related protein

hetero molecules

A: Exopolyphosphatase-related protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	39.994, 39.994, 295.489
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-150- HOH

#1: Protein	Exopolyphosphatase-related protein Mass: 15563.288 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_2029 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28250
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.27 Å³/Da / Density % sol: 45.9 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG MME 5000, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2009

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 19804 / % possible obs: 99.2 % / Redundancy: 6.1 % / R_merge(I) obs: 0.062 / Χ²: 1.475 / Net I/σ(I): 8.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.6-1.66	6.2	0.43	1898	0.835	1	99.8
1.66-1.72	6.2	0.3	1905	0.858	1	99.5
1.72-1.8	6.2	0.215	1907	0.899	1	99.8
1.8-1.9	6.1	0.166	1944	0.983	1	99.7
1.9-2.02	6.2	0.117	1931	1.038	1	99.7
2.02-2.17	6.2	0.082	1957	1.18	1	99.6
2.17-2.39	6.2	0.071	1977	1.343	1	99.8
2.39-2.74	6.2	0.071	2011	1.904	1	99.9
2.74-3.45	6	0.062	2075	2.597	1	100
3.45-50	5.8	0.047	2199	2.94	1	94.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 1.7→29.88 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.94 / SU B: 4.829 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	849	5.1 %	RANDOM
R_work	0.21	-	-	-
obs	0.212	16627	99.32 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 10.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→29.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	988	0	5	59	1052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	1034
X-RAY DIFFRACTION	r_angle_refined_deg	1.291	1.996	1408
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.106	5	143
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.243	25.75	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.114	15	185
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.146	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	172
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	755
X-RAY DIFFRACTION	r_mcbond_it	0.621	1.5	676
X-RAY DIFFRACTION	r_mcangle_it	1.046	2	1085
X-RAY DIFFRACTION	r_scbond_it	2.019	3	358
X-RAY DIFFRACTION	r_scangle_it	3.232	4.5	317

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	66	-
R_work	0.263	1136	-
all	-	1202	-
obs	-	-	99.75 %

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	8.9198	3.3546	2.0359	7.7238	1.3313	4.9626	-0.0494	0.2123	-0.443	0.1395	0.1295	0.0219	0.9486	-0.0136	-0.0802	0.2891	0.044	0.0098	0.0765	-0.0403	0.1257	9.3065	11.9061	10.156
2	2.1139	1.2698	-1.4552	14.9821	-7.0251	28.7299	-0.4933	-0.1995	-0.1372	-0.0236	0.1814	-0.2678	1.391	1.7084	0.3119	0.4711	0.2892	0.0323	0.228	-0.0023	0.1174	13.2124	17.1304	21.2265
3	10.2585	4.1271	0.3341	6.8819	-2.5942	5.9917	-0.1084	-0.4497	-0.0624	-0.2035	0.2757	0.129	0.5758	-0.3776	-0.1673	0.4624	0.0613	0.034	0.1792	0.0288	0.2441	6.7551	10.951	20.6123
4	3.409	2.9232	-2.4741	2.9861	0.9103	21.5943	-0.0257	0.1942	0.0756	0.0503	0.1553	0.0834	1.374	-0.7389	-0.1296	0.6213	0.0051	-0.0251	0.1455	0.057	0.3512	5.1341	5.9465	15.8435
5	10.3367	3.6035	3.342	8.7568	2.6822	2.3111	-0.1758	-0.5107	0.2593	0.2344	0.1516	-0.6493	0.3251	0.3552	0.0241	0.2965	0.2431	-0.0726	0.3717	-0.067	0.2169	21.2383	14.9602	15.0502
6	10.5089	3.9303	-1.8431	18.2815	-3.7036	0.8649	-0.3901	-0.227	0.1706	1.0271	0.3239	-0.4101	-0.1255	-0.0138	0.0662	0.4683	0.2649	-0.0779	0.2734	-0.032	0.2187	21.2858	9.4098	19.501
7	7.3477	4.672	-2.1389	3.1895	-2.0218	4.5995	-0.3552	0.3384	0.0634	-0.2877	0.3635	0.2071	0.857	-0.0461	-0.0083	0.4045	0.2287	-0.0049	0.2594	0.0731	0.332	16.3614	6.7973	16.8702
8	3.1363	4.3825	-3.2408	6.8793	-4.2669	3.4546	-0.0235	-0.3683	-0.1045	0.2023	-0.0143	-0.461	0.1153	0.5986	0.0379	0.1683	0.1602	-0.0406	0.5108	-0.0949	0.244	21.0587	19.4131	7.4109
9	9.6627	-0.0551	-4.7703	4.1332	-0.3674	12.204	0.0472	0.2319	0.1136	-0.0989	0.0194	-0.0142	-0.0109	0.0125	-0.0665	0.0661	0.0233	0.0047	0.0989	-0.0408	0.1131	17.2444	17.8269	0.5543
10	52.7576	2.0388	-18.187	2.4141	-1.7341	6.9744	-1.1254	1.9865	-1.8016	-0.0595	0.3146	-0.1762	0.6719	-0.8249	0.8108	0.4381	-0.0906	0.0685	0.2576	-0.152	0.267	9.9734	11.3338	1.4755
11	5.6142	1.041	0.4275	3.2961	1.3149	6.1937	-0.1064	0.0924	-0.1201	0.2468	0.2064	0.0171	0.4112	0.2226	-0.1	0.0943	0.0396	0.0006	0.0269	-0.0219	0.0914	8.6336	19.735	12.645
12	9.3351	-1.8984	-2.4339	11.3098	3.5549	16.546	0.0602	-0.0836	0.5665	0.06	0.2353	-0.6464	-0.3699	0.7261	-0.2956	0.0846	0.0017	-0.014	0.1093	-0.0587	0.2031	15.2067	29.5395	13.1563
13	6.8634	-3.4415	0.2035	4.5621	0.9551	10.792	0.01	0.0858	0.3916	-0.0498	0.1087	-0.335	-0.3869	0.298	-0.1187	0.0596	-0.0097	0.0168	0.0755	-0.0179	0.1231	13.587	27.6171	5.8504
14	5.3958	1.9246	-1.5744	3.9328	-0.9702	2.742	0.0137	0.5006	-0.0607	-0.2098	0.0442	-0.0123	0.0161	-0.0264	-0.0579	0.0518	0.0145	-0.0008	0.1281	-0.0179	0.0686	9.5162	21.7367	-0.3461
15	1.8682	-0.2695	-0.8317	2.1085	2.5193	5.8141	-0.0156	0.0175	0.1986	0.1063	-0.0641	0.0517	-0.1073	-0.1927	0.0797	0.084	0.0369	0.0005	0.0294	-0.0195	0.0969	6.0458	25.5265	12.792
16	5.5939	-9.8867	-1.3042	18.244	-0.7741	12.8095	0.0153	-0.0788	0.1298	0.1344	0.2778	-0.1034	-0.6673	-0.487	-0.2931	0.1821	0.0587	-0.0214	0.0919	0.0094	0.3571	4.7518	36.1816	13.0507
17	7.8413	-0.2239	-0.9464	7.8345	0.4748	10.432	0.059	0.1522	0.3932	-0.3816	0.0091	0.1398	-0.8632	-0.243	-0.068	0.1362	0.0491	-0.0043	0.0797	0.0154	0.1542	5.5308	32.5668	6.872
18	0.6871	-0.6275	-1.7326	0.7155	2.8775	16.7072	0.0201	0.0601	-0.0031	-0.0207	-0.0549	0.0238	-0.281	-0.3225	0.0348	0.0969	0.0399	0.0163	0.0776	-0.0155	0.1353	2.1007	27.4609	16.3623
19	10.6491	2.3489	-3.6171	8.7561	2.3265	15.9007	0.0731	0.1916	0.0376	-0.3892	-0.0713	0.4711	-0.1246	-1.248	-0.0018	0.1075	0.0635	-0.0039	0.1578	-0.0121	0.1389	-3.196	27.2401	28.745
20	19.6476	0.0254	-8.4659	20.528	1.6143	12.8821	0.1008	-0.8299	-0.7584	0.7746	-0.2242	0.3218	0.9858	-0.3402	0.1233	0.2183	-0.0322	-0.0109	0.3269	0.0095	0.2225	-6.9201	23.2377	34.5605

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 13
2	X-RAY DIFFRACTION	2	A	14 - 20
3	X-RAY DIFFRACTION	3	A	21 - 25
4	X-RAY DIFFRACTION	4	A	26 - 32
5	X-RAY DIFFRACTION	5	A	33 - 40
6	X-RAY DIFFRACTION	6	A	41 - 47
7	X-RAY DIFFRACTION	7	A	48 - 53
8	X-RAY DIFFRACTION	8	A	54 - 59
9	X-RAY DIFFRACTION	9	A	60 - 64
10	X-RAY DIFFRACTION	10	A	65 - 71
11	X-RAY DIFFRACTION	11	A	72 - 79
12	X-RAY DIFFRACTION	12	A	80 - 84
13	X-RAY DIFFRACTION	13	A	85 - 90
14	X-RAY DIFFRACTION	14	A	91 - 96
15	X-RAY DIFFRACTION	15	A	97 - 105
16	X-RAY DIFFRACTION	16	A	106 - 110
17	X-RAY DIFFRACTION	17	A	111 - 115
18	X-RAY DIFFRACTION	18	A	116 - 127
19	X-RAY DIFFRACTION	19	A	128 - 132
20	X-RAY DIFFRACTION	20	A	133 - 138

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