PDB-2a3q: X-Ray Structure of Protein from Mus Musculus MM.29898

ID or keywords:

Entry

Database: PDB / ID: 2a3q

Title

X-Ray Structure of Protein from Mus Musculus MM.29898

Components

hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MM.29898 / BC004623 / 2410015N17RIK /

PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

dCTP catabolic process /

dCTP diphosphatase /

dCTP diphosphatase activity / pyrimidine deoxyribonucleotide binding / nucleoside triphosphate catabolic process /

pyrophosphatase activity / nucleoside triphosphate diphosphatase activity / DNA protection / magnesium ion binding /

nucleoplasm ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.32 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be Published
Title: X-Ray Structure of Protein from Mus Musculus MM.29898
Authors: Center for Eukaryotic Structural Genomics (CESG)

History

Deposition	Jun 25, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 19, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2a3q.cif.gz	58.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2a3q.ent.gz	44.5 KB	Display	PDB format
PDBx/mmJSON format	2a3q.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/a3/2a3q ftp://data.pdbj.org/pub/pdb/validation_reports/a3/2a3q	HTTPS FTP

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Related structure data

Similar structure data	6s60-2 2q4p-d 4a63-6 6uyc-1 5wmt-2 6m88-d 2xc5-d 6l9f-2 5ar1-d 6zqt-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: GO.34455

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: hypothetical protein

B: hypothetical protein

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

1

Idetical with deposited unit
defined by author&software

2

A: hypothetical protein

B: hypothetical protein

A: hypothetical protein

B: hypothetical protein

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

Unit cell

Length a, b, c (Å)	73.541, 73.541, 236.078
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 22 - 130 / Label seq-ID: 22 - 130

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	hypothetical protein / Mass: 18910.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: MM.29898 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: GenBank: 12963573, UniProt: Q9QY93*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 49.6 %
Crystal grow	Temperature: 277 K / pH: 5 Details: 10 MG/ML PROTEIN, 18% MEPEG 2K, 0.100 M SODIUM CITRATE, 0.100 M SODIUM ACETATE, vapor diffusion, hanging drop, temperature 277K, pH 5.00

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.96802, 0.96411

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.96802	1
2	0.96411	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	D res high (Å)	% possible obs
13.2	1	17029	0.061	1.072	2.35	98.5
10.7	2	15860	0.056	1.06	2.4	97.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.79	50	89.7	1	0.041	1.068	10.3
4.6	5.79	97.2	1	0.045	1.106	12.6
4.02	4.6	96.8	1	0.052	1.099	12.2
3.65	4.02	99.2	1	0.054	1.006	13.1
3.39	3.65	98.1	1	0.059	1.145	12.6
3.19	3.39	99.5	1	0.078	1.088	13.2
3.03	3.19	99.6	1	0.091	1.231	13.5
2.9	3.03	99.9	1	0.11	1.216	13.7
2.79	2.9	100	1	0.129	1.177	13.8
2.69	2.79	100	1	0.16	1.161	13.9
2.61	2.69	100	1	0.221	1.021	14
2.53	2.61	100	1	0.272	0.974	14
2.46	2.53	100	1	0.344	0.928	14
2.4	2.46	100	1	0.381	0.953	13.6
2.35	2.4	100	1	0.446	0.901	13.1
5.92	50	86.6	2	0.03	0.945	8.3
4.7	5.92	94.3	2	0.038	0.933	10.4
4.1	4.7	94.3	2	0.048	0.959	10.1
3.73	4.1	97	2	0.051	0.881	10.8
3.46	3.73	96.8	2	0.053	0.937	10.3
3.26	3.46	98.2	2	0.072	0.991	10.6
3.09	3.26	98.9	2	0.087	1.163	10.9
2.96	3.09	98.9	2	0.108	1.325	11.1
2.85	2.96	99.1	2	0.139	1.203	11.2
2.75	2.85	99.4	2	0.155	1.22	11.3
2.66	2.75	99.5	2	0.226	1.121	11.2
2.59	2.66	100	2	0.294	1.045	11.3
2.52	2.59	99.6	2	0.363	1.047	11.3
2.46	2.52	99.7	2	0.461	1.02	11
2.4	2.46	99.9	2	0.47	1.034	10.4

Reflection

Resolution: 2.35→50 Å / Num. obs: 17029 / % possible obs: 98.5 % / Redundancy: 13.2 % / R_merge(I) obs: 0.061 / Net I/σ(I): 16.785

Reflection shell

Resolution: 2.35→2.4 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.446 / Mean I/σ(I) obs: 5.272 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 2.32 Å / Lowest resolution: 37.93 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	13444	3273
ISO_2	0.812	0.805	0.67	0.693	12529	2994
ANO_1	0.816	0	0.814	0	13411	0
ANO_2	0.918	0	0.655	0	12317	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	10.04-37.93	0	0	0	0	94	120
ISO_1	7.22-10.04	0	0	0	0	222	137
ISO_1	5.93-7.22	0	0	0	0	317	151
ISO_1	5.16-5.93	0	0	0	0	389	159
ISO_1	4.62-5.16	0	0	0	0	445	156
ISO_1	4.22-4.62	0	0	0	0	502	158
ISO_1	3.91-4.22	0	0	0	0	552	163
ISO_1	3.66-3.91	0	0	0	0	606	170
ISO_1	3.45-3.66	0	0	0	0	655	164
ISO_1	3.28-3.45	0	0	0	0	680	169
ISO_1	3.13-3.28	0	0	0	0	743	169
ISO_1	3-3.13	0	0	0	0	768	167
ISO_1	2.88-3	0	0	0	0	822	164
ISO_1	2.77-2.88	0	0	0	0	851	167
ISO_1	2.68-2.77	0	0	0	0	897	174
ISO_1	2.6-2.68	0	0	0	0	904	178
ISO_1	2.52-2.6	0	0	0	0	952	178
ISO_1	2.45-2.52	0	0	0	0	975	167
ISO_1	2.38-2.45	0	0	0	0	1028	183
ISO_1	2.32-2.38	0	0	0	0	1042	179
ANO_1	10.04-37.93	0.713	0	0.951	0	85	0
ANO_1	7.22-10.04	0.646	0	1.292	0	217	0
ANO_1	5.93-7.22	0.523	0	1.673	0	317	0
ANO_1	5.16-5.93	0.618	0	1.507	0	389	0
ANO_1	4.62-5.16	0.726	0	1.286	0	442	0
ANO_1	4.22-4.62	0.832	0	0.914	0	499	0
ANO_1	3.91-4.22	0.871	0	0.824	0	548	0
ANO_1	3.66-3.91	0.859	0	0.894	0	606	0
ANO_1	3.45-3.66	0.906	0	0.682	0	651	0
ANO_1	3.28-3.45	0.947	0	0.547	0	676	0
ANO_1	3.13-3.28	0.941	0	0.496	0	743	0
ANO_1	3-3.13	0.962	0	0.391	0	767	0
ANO_1	2.88-3	0.974	0	0.309	0	822	0
ANO_1	2.77-2.88	0.985	0	0.245	0	851	0
ANO_1	2.68-2.77	0.991	0	0.174	0	897	0
ANO_1	2.6-2.68	0.996	0	0.132	0	904	0
ANO_1	2.52-2.6	0.998	0	0.099	0	952	0
ANO_1	2.45-2.52	0.999	0	0.075	0	975	0
ANO_1	2.38-2.45	1	0	0.052	0	1028	0
ANO_1	2.32-2.38	1	0	0.036	0	1042	0
ISO_2	10.04-37.93	0.63	0.577	1.132	1.289	88	109
ISO_2	7.22-10.04	0.681	0.815	1.145	1.069	210	125
ISO_2	5.93-7.22	0.695	0.725	1.58	1.213	309	141
ISO_2	5.16-5.93	0.708	0.81	1.165	0.92	385	147
ISO_2	4.62-5.16	0.78	0.767	0.848	0.627	435	149
ISO_2	4.22-4.62	0.829	0.818	0.609	0.485	496	146
ISO_2	3.91-4.22	0.848	0.901	0.551	0.454	543	153
ISO_2	3.66-3.91	0.863	0.858	0.532	0.398	603	161
ISO_2	3.45-3.66	0.854	0.898	0.419	0.303	650	157
ISO_2	3.28-3.45	0.924	0.934	0.4	0.288	675	161
ISO_2	3.13-3.28	0.866	0.867	0.343	0.229	740	160
ISO_2	3-3.13	0.87	0.89	0.289	0.204	766	162
ISO_2	2.88-3	0.899	0.914	0.24	0.169	821	159
ISO_2	2.77-2.88	0.886	0.882	0.179	0.124	850	166
ISO_2	2.68-2.77	0.89	0.928	0.143	0.088	897	169
ISO_2	2.6-2.68	0.881	0.946	0.108	0.073	903	173
ISO_2	2.52-2.6	0.885	0.9	0.08	0.047	952	174
ISO_2	2.45-2.52	0.869	0.919	0.056	0.038	975	164
ISO_2	2.38-2.45	0.87	0.898	0.041	0.03	1028	183
ISO_2	2.32-2.38	0.852	0.972	0.033	0.028	203	35
ANO_2	10.04-37.93	0.632	0	1.504	0	80	0
ANO_2	7.22-10.04	0.654	0	1.702	0	190	0
ANO_2	5.93-7.22	0.562	0	1.969	0	295	0
ANO_2	5.16-5.93	0.73	0	1.677	0	369	0
ANO_2	4.62-5.16	0.838	0	1.265	0	418	0
ANO_2	4.22-4.62	0.892	0	0.855	0	474	0
ANO_2	3.91-4.22	0.927	0	0.674	0	531	0
ANO_2	3.66-3.91	0.946	0	0.753	0	594	0
ANO_2	3.45-3.66	0.959	0	0.553	0	638	0
ANO_2	3.28-3.45	0.974	0	0.435	0	666	0
ANO_2	3.13-3.28	0.97	0	0.355	0	731	0
ANO_2	3-3.13	0.979	0	0.262	0	758	0
ANO_2	2.88-3	0.988	0	0.2	0	813	0
ANO_2	2.77-2.88	0.993	0	0.147	0	841	0
ANO_2	2.68-2.77	0.996	0	0.109	0	889	0
ANO_2	2.6-2.68	0.998	0	0.075	0	903	0
ANO_2	2.52-2.6	0.999	0	0.058	0	948	0
ANO_2	2.45-2.52	1	0	0.042	0	975	0
ANO_2	2.38-2.45	1	0	0.032	0	1010	0
ANO_2	2.32-2.38	1	0	0.025	0	194	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-11.247	30.776	123.88	SE	105.79	0.64
2	-5.348	35.897	195.051	SE	99.94	0.67

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 16962

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.57-100	60.2	0.848	507
6.04-7.57	59.5	0.887	502
5.26-6.04	60.2	0.883	512
4.78-5.26	64.5	0.889	514
4.43-4.78	68.7	0.912	506
4.16-4.43	68.2	0.894	501
3.95-4.16	67.2	0.886	512
3.77-3.95	72.5	0.856	534
3.61-3.77	74.7	0.852	555
3.47-3.61	75.7	0.837	563
3.34-3.47	74	0.84	574
3.23-3.34	76.4	0.791	625
3.13-3.23	80	0.803	642
3.04-3.13	80	0.789	640
2.95-3.04	81.8	0.777	668
2.88-2.95	81.2	0.734	705
2.8-2.88	85.9	0.729	701
2.74-2.8	86.6	0.775	711
2.67-2.74	86.6	0.754	738
2.62-2.67	90.1	0.695	761
2.56-2.62	84.2	0.7	772
2.51-2.56	89.4	0.699	781
2.46-2.51	88.7	0.729	775
2.42-2.46	88.5	0.721	836
2.37-2.42	92.2	0.761	798
2.32-2.37	89.1	0.652	1029

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.6	data extraction
SOLOMON		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.32→43.27 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.932 / SU B: 13.588 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	858	5.1 %	RANDOM
R_work	0.21	-	-	-
obs	0.212	16081	98.5 %	-

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: 68.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	0.07 Å²	0 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	-0.22 Å²

Refinement step

Cycle: LAST / Resolution: 2.32→43.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1813	0	0	24	1837

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	1864
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.834	1.96	2538
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.471	5	220
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.548	23.636	99
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.919	15	303
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.246	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	270
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1462
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	1020
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	1284
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	67
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	0.236	0.2	63
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.154	0.2	8
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	0.974	1.5	1152
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.581	2	1811
X-RAY DIFFRACTION	r_scbond_it	2.865	3	806
X-RAY DIFFRACTION	r_scangle_it	4.306	4.5	727
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
436	tight positional	0.24	0.2
455	medium positional	0.75	0.5
436	tight thermal	0.21	0.5
455	medium thermal	1.11	2

LS refinement shell

Resolution: 2.32→2.38 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.252	56	-
R_work	0.218	1171	-
obs	-	-	99.92 %

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	9.7524	3.1123	-0.037	4.2116	0.6732	4.1246	-0.2557	-0.0495	0.5121	-0.1024	0.1522	0.3717	-0.3325	-0.5179	0.1034	-0.3631	0.0349	0.0414	0.2339	-0.4076	-0.1298	25.207	32.13	112.422
2	14.6458	4.5729	1.3629	6.2679	2.6586	2.6351	-0.26	-0.2528	-0.8661	0.3132	0.3056	-0.7358	0.4855	0.2074	-0.0455	-0.2948	-0.0158	-0.0343	0.3462	-0.2681	-0.1842	44.886	23.013	118.327
3	5.842	0.9059	-0.3761	3.8307	1.0562	5.0154	-0.2685	-0.4382	0.0471	-0.2677	0.0438	-0.1232	0.0487	0.0423	0.2247	-0.3858	-0.0158	0.0836	-0.0658	-0.2576	-0.3089	37.352	24.444	105.668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	112 - 134	112 - 134
2	X-RAY DIFFRACTION	1	B	B	22 - 52	22 - 52
3	X-RAY DIFFRACTION	2	B	B	112 - 130	112 - 130
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