PDB-3hqx: Crystal structure of protein of unknown function (DUF1255,PF06865...

ID or keywords:

Entry

Database: PDB / ID: 3hqx

Title

Crystal structure of protein of unknown function (DUF1255,PF06865) from Acinetobacter sp. ADP1

Components

UPF0345 protein ACIAD0356

Keywords

structural genomics / unknown function / DUF1255 / PF06865 / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

pyrimidine-nucleoside phosphorylase / thymidine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function

Biological species

Acinetobacter sp. ADP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.66 Å

Authors

Nocek, B. / Hatzos, C. / Freeman, L. / Dauter, Z. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of protein of unknown function (DUF1255,PF06865) from Acinetobacter sp. ADP1
Authors: Nocek, B. / Hatzos, C. / Freeman, L. / Dauter, Z. / Joachimiak, A.

History

Deposition	Jun 8, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 30, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3hqx.cif.gz	37.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3hqx.ent.gz	26.1 KB	Display	PDB format
PDBx/mmJSON format	3hqx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hqx_validation.pdf.gz	421.1 KB	Display	wwPDB validaton report
Full document	3hqx_full_validation.pdf.gz	421.3 KB	Display
Data in XML	3hqx_validation.xml.gz	8.3 KB	Display
Data in CIF	3hqx_validation.cif.gz	10.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hq/3hqx ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqx	HTTPS FTP

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Related structure data

Similar structure data	6mjo-d 6m4u-1 3ktm-10 5oqd-2 5v5g-1 2hjd-1 4gio-d 3phw-1 5yjd-1 3bd4-d 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: apc86610

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UPF0345 protein ACIAD0356

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

1

A: UPF0345 protein ACIAD0356

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

Unit cell

Length a, b, c (Å)	65.050, 25.952, 55.230
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

Unknown

#1: Protein	UPF0345 protein ACIAD0356 Mass: 12451.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. ADP1 (bacteria) / Gene: ACIAD0356 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q6FF51
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.87 Å³/Da / Density % sol: 34.29 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% Peg 3350 .2 M Lithium sulfate 0.1 M Hepes pH7.5, 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: 0.9794 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 14, 2009 / Details: double crystal
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.65→25.5 Å / Num. all: 11655 / Num. obs: 11471 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / B_iso Wilson estimate: 29.5 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 51
Reflection shell	Resolution: 1.65→1.72 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.115 / Mean I/σ(I) obs: 13 / Num. unique all: 1094 / % possible all: 95.3

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELX		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.66→25.5 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.946 / SU B: 3.746 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2015	545	4.8 %	RANDOM
R_work	0.16278	-	-	-
all	0.17	11446	-	-
obs	0.16471	10901	98.27 %	-

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 mean: 8.882 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.45 Å²	0 Å²	0 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	1.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→25.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	829	0	0	102	931

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	846
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	564
X-RAY DIFFRACTION	r_angle_refined_deg	1.596	1.956	1145
X-RAY DIFFRACTION	r_angle_other_deg	0.914	3	1385
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.077	5	104
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.495	24.872	39
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.05	15	147
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.505	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	132
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	932
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	167
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.143	1.5	521
X-RAY DIFFRACTION	r_mcbond_other	0.35	1.5	212
X-RAY DIFFRACTION	r_mcangle_it	1.954	2	851
X-RAY DIFFRACTION	r_scbond_it	2.623	3	325
X-RAY DIFFRACTION	r_scangle_it	4.104	4.5	294
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.659→1.702 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.147	39	-
R_work	0.188	748	-
obs	-	-	92.7 %

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	0.0558	-0.4214	-0.3841	10.0506	4.6372	3.3637	0.0242	0.0416	0.0007	-0.2515	-0.0848	0.0143	-0.2002	-0.046	0.0606	0.0998	0.0148	-0.0014	0.1651	0.0085	0.1353	2.7494	4.9026	25.7684
2	3.9191	-0.5591	4.379	0.5201	-1.1172	5.9108	-0.0345	0.0704	-0.0603	0.1436	-0.0495	-0.0798	-0.108	0.1192	0.084	0.1023	-0.0102	0.0068	0.0862	0.0055	0.1072	3.1041	-6.6954	39.9448
3	2.4607	0.572	3.4524	1.0647	1.3147	11.7342	-0.0196	-0.2253	-0.0719	0.1434	-0.0295	-0.0245	0.0421	-0.1028	0.0491	0.1076	-0.0042	0.0029	0.0996	0.006	0.1149	3.7766	-2.3082	44.1963
4	3.5957	1.1963	-5.7609	2.4518	0.6261	22.4256	-0.0048	0.1507	-0.0062	-0.1802	0.0266	0.0407	0.1196	-0.273	-0.0217	0.1017	0.0102	-0.007	0.1222	-0.0037	0.1454	6.4217	-2.7188	26.1358
5	1.3902	-0.7905	-2.8675	1.4115	3.1048	12.6477	-0.0423	-0.0144	-0.0989	0.1124	-0.0014	-0.0495	0.2457	0.1461	0.0437	0.081	-0.0092	-0.0055	0.0789	0.0116	0.1103	7.9081	0.6513	37.1172
6	2.6111	-1.1791	-0.509	8.7255	4.9478	8.5229	-0.1472	-0.5343	-0.0896	0.5668	-0.054	-0.2185	0.2041	-0.1156	0.2011	0.1709	-0.0406	-0.0615	0.1901	0.0393	0.1031	12.8228	1.3407	54.1146
7	0.9833	-2.1873	1.0213	6.5355	-1.1751	1.784	0.078	0.0197	0.1574	-0.1355	-0.2372	-0.3954	0.0986	-0.1057	0.1592	0.0949	-0.0272	0.0052	0.1322	0.0469	0.2074	19.1937	-5.1964	40.0245
8	5.9278	1.1999	-0.9895	5.256	1.5461	2.8707	0.0978	0.0865	-0.264	-0.1056	-0.1832	-0.4527	-0.0984	0.0436	0.0854	0.0779	-0.0247	0.0008	0.1089	0.019	0.1233	14.7081	5.5576	36.412
9	3.5683	-0.3645	2.7366	3.3992	-1.5835	2.6057	0.0393	-0.0592	0.0228	0.2446	-0.1266	-0.1784	-0.0712	-0.0041	0.0873	0.1196	-0.0212	-0.023	0.1175	0.0097	0.1021	11.7124	11.1723	45.1928
10	6.3223	0.7697	-3.1539	10.0327	5.0924	6.9998	-0.28	-0.3676	-0.504	0.8054	0.1302	-1.0982	0.2858	0.8894	0.1498	0.1723	-0.012	-0.1048	0.2474	0.0945	0.3186	25.4097	4.1841	48.4555
11	5.3739	-3.4158	2.3022	7.4287	-2.0513	5.5023	-0.0054	-0.1873	0.025	0.3623	-0.1052	-0.4333	-0.2041	0.3759	0.1106	0.0976	-0.0475	-0.0458	0.1473	0.0307	0.1142	18.0738	12.6799	46.1571
12	5.9641	-4.0097	-2.3356	6.437	1.4332	2.9312	-0.0504	-0.0897	-0.1239	0.0858	-0.1252	-0.3731	0.0572	0.0965	0.1755	0.0552	-0.0312	-0.0076	0.0959	0.0434	0.1422	18.7355	7.4047	38.1959
13	9.7745	-6.512	-5.4044	7.7518	4.7506	4.994	-0.0665	-0.3623	0.0574	0.2893	0.1481	-0.645	0.1145	0.26	-0.0816	0.1035	-0.0354	-0.0393	0.1174	0.0576	0.1767	18.5951	0.8624	46.1981
14	5.967	-0.0024	2.7736	4.2833	0.2659	10.6553	-0.0093	-0.4294	0.2533	0.2687	-0.061	0.0567	-0.3155	-0.3407	0.0703	0.1073	-0.0111	0.0025	0.1042	0.004	0.1035	5.5236	9.4125	46.9082
15	9.8302	-0.5074	-4.8387	6.204	-0.5799	8.3145	-0.1486	-0.0317	-0.4919	-0.1589	-0.0321	-0.2917	0.3588	0.3373	0.1807	0.0674	-0.0134	-0.0088	0.0848	0.0018	0.102	11.9996	2.1135	35.026

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 10
2	X-RAY DIFFRACTION	2	A	11 - 19
3	X-RAY DIFFRACTION	3	A	20 - 26
4	X-RAY DIFFRACTION	4	A	27 - 31
5	X-RAY DIFFRACTION	5	A	32 - 44
6	X-RAY DIFFRACTION	6	A	45 - 49
7	X-RAY DIFFRACTION	7	A	50 - 55
8	X-RAY DIFFRACTION	8	A	56 - 60
9	X-RAY DIFFRACTION	9	A	61 - 67
10	X-RAY DIFFRACTION	10	A	68 - 73
11	X-RAY DIFFRACTION	11	A	74 - 79
12	X-RAY DIFFRACTION	12	A	80 - 87
13	X-RAY DIFFRACTION	13	A	88 - 96
14	X-RAY DIFFRACTION	14	A	97 - 101
15	X-RAY DIFFRACTION	15	A	102 - 106

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