PDB-3c9q: Crystal structure of the uncharacterized human protein C8orf32 wi...

ID or keywords:

Entry

Database: PDB / ID: 3c9q

Title

Crystal structure of the uncharacterized human protein C8orf32 with bound peptide

Components

Synthetic peptide
Uncharacterized protein C8orf32

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Medically relevant / putative involvement in human inherited ataxias and disorders of Purkinje cell degeneration / candidate gene important in the pathogenesis of T-cell prolymphocytic leukemia / gene associated with CRE-pathway activation / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

protein N-terminal glutamine amidohydrolase / protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / protein modification process / nucleus / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Bitto, E. / Bingman, C.A. / McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be Published
Title: Crystal structure of the uncharacterized human protein C8orf32 with bound peptide.
Authors: Bitto, E. / Bingman, C.A. / McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N.

History

Deposition	Feb 18, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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	3c9q.cif.gz	65.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3c9q.ent.gz	47.1 KB	Display	PDB format
PDBx/mmJSON format	3c9q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3c9q_validation.pdf.gz	470.4 KB	Display	wwPDB validaton report
Full document	3c9q_full_validation.pdf.gz	472.7 KB	Display
Data in XML	3c9q_validation.xml.gz	14.9 KB	Display
Data in CIF	3c9q_validation.cif.gz	21.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/3c9q ftp://data.pdbj.org/pub/pdb/validation_reports/c9/3c9q	HTTPS FTP

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Related structure data

Similar structure data	5g00-d 6di8-2 4boe-d 3bx8-3 1lay-d 2a6w-1 1z2w-2 5fnx-d 4j25-1 4e07-2 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.39772

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1)

Deposited unit

A: Uncharacterized protein C8orf32

L: Synthetic peptide

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	34.322, 64.039, 113.660
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

THE BIOLOGICAL UNIT IS THE MONOMERIC COMPLEX OF THE PROTEIN C8ORF32 (CHAIN A) WITH BOUND PEPTIDE (CHAIN L)

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Protein / Protein/peptide , 2 types, 2 molecules AL

#1: Protein	Uncharacterized protein C8orf32 Mass: 23721.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C8orf32 / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q96HA8
#2: Protein/peptide	Synthetic peptide Mass: 277.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide

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Non-polymers , 4 types, 283 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CO3 / CARBONATE ION Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.6 Å³/Da / Density % sol: 52.73 %
Crystal grow	Temperature: 291 K Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.003 M Sodium azide, 0.0003 M TCEP, Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (1% Ethylene glycol, 1.8 ...Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.003 M Sodium azide, 0.0003 M TCEP, Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (1% Ethylene glycol, 1.8 M Ammonium sulfate, 0.10 M MES pH 6.0). Cryoprotected in four stages with well solution using 0 to 25 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal

Density Matthews: 2.6 Å³/Da / Density % sol: 52.73 %

Crystal grow

Temperature: 291 K
Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.003 M Sodium azide, 0.0003 M TCEP, Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (1% Ethylene glycol, 1.8 ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97942

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY

Radiation

Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97942 Å / Relative weight: 1

Reflection

Resolution: 1.498→32.857 Å / Num. obs: 40943 / % possible obs: 99.5 % / Redundancy: 12.2 % / R_merge(I) obs: 0.105 / Net I/σ(I): 12.075

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.498-1.53	6.9	0.543	2.526	2566	0.974	95.9
1.53-1.57	8.1	0.474		2650	0.988	97.7
1.57-1.62	9.5	0.455		2674	0.99	99.2
1.62-1.66	11	0.433		2689	1	100
1.66-1.72	12.3	0.382		2725	1.108	100
1.72-1.78	13	0.336		2687	1.122	100
1.78-1.85	13.5	0.277		2706	1.172	100
1.85-1.93	13.6	0.215		2722	1.238	100
1.93-2.04	13.6	0.172		2733	1.26	100
2.04-2.16	13.7	0.135		2733	1.277	100
2.16-2.33	13.7	0.118		2740	1.334	100
2.33-2.56	13.8	0.109		2760	1.355	100
2.56-2.94	13.5	0.086		2769	1.32	100
2.94-3.7	13.3	0.063		2817	1.22	100
3.7-32.857	12.6	0.058		2972	1.23	99.5

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Phasing

Phasing

Method:

SAD

Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.5 Å / Lowest resolution: 32.86 Å / Power centric: 0

ID	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	0	0	36238	4556
ANO_1	0.645	1.771	35978	0

Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	6.58-32.86	0	0	345	217
ISO_1	4.7-6.58	0	0	687	230
ISO_1	3.85-4.7	0	0	909	223
ISO_1	3.34-3.85	0	0	1117	234
ISO_1	2.99-3.34	0	0	1274	229
ISO_1	2.73-2.99	0	0	1410	231
ISO_1	2.53-2.73	0	0	1534	226
ISO_1	2.37-2.53	0	0	1652	229
ISO_1	2.23-2.37	0	0	1792	232
ISO_1	2.12-2.23	0	0	1881	235
ISO_1	2.02-2.12	0	0	1981	216
ISO_1	1.94-2.02	0	0	2093	238
ISO_1	1.86-1.94	0	0	2187	236
ISO_1	1.79-1.86	0	0	2258	226
ISO_1	1.73-1.79	0	0	2333	222
ISO_1	1.68-1.73	0	0	2439	242
ISO_1	1.63-1.68	0	0	2515	231
ISO_1	1.58-1.63	0	0	2599	223
ISO_1	1.54-1.58	0	0	2606	230
ISO_1	1.5-1.54	0	0	2626	206
ANO_1	6.58-32.86	0.393	3.336	345	0
ANO_1	4.7-6.58	0.4	3.281	687	0
ANO_1	3.85-4.7	0.522	2.528	907	0
ANO_1	3.34-3.85	0.464	2.899	1117	0
ANO_1	2.99-3.34	0.426	3.124	1272	0
ANO_1	2.73-2.99	0.4	3.315	1408	0
ANO_1	2.53-2.73	0.41	3.244	1534	0
ANO_1	2.37-2.53	0.427	3.075	1652	0
ANO_1	2.23-2.37	0.451	2.846	1792	0
ANO_1	2.12-2.23	0.496	2.453	1881	0
ANO_1	2.02-2.12	0.544	2.247	1981	0
ANO_1	1.94-2.02	0.59	1.951	2093	0
ANO_1	1.86-1.94	0.649	1.75	2187	0
ANO_1	1.79-1.86	0.724	1.467	2258	0
ANO_1	1.73-1.79	0.758	1.313	2333	0
ANO_1	1.68-1.73	0.822	1.151	2439	0
ANO_1	1.63-1.68	0.854	0.975	2511	0
ANO_1	1.58-1.63	0.888	0.861	2565	0
ANO_1	1.54-1.58	0.918	0.825	2524	0
ANO_1	1.5-1.54	0.938	0.718	2492	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	3.974	58.562	67.447	SE	11.27	1.13
2	9.054	23.537	91.296	SE	12	1.06
3	5.472	28.398	106.564	SE	11.2	0.91
4	3.398	63.046	83.004	SE	23.19	0.68

Phasing dm

Method: Solvent flattening and histogram matching / Reflection: 40794

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.84-100	63.8	0.693	503
5.24-6.84	60.5	0.897	581
4.4-5.24	53.5	0.928	705
3.87-4.4	54.3	0.936	796
3.5-3.87	53.7	0.933	884
3.21-3.5	54.4	0.923	968
2.99-3.21	56.7	0.913	1050
2.8-2.99	50	0.923	1091
2.65-2.8	53.4	0.922	1157
2.52-2.65	53.2	0.914	1242
2.41-2.52	53.4	0.918	1275
2.31-2.41	53.4	0.924	1347
2.22-2.31	54.3	0.914	1390
2.14-2.22	52.9	0.922	1405
2.07-2.14	53.4	0.916	1518
2.01-2.07	55.6	0.916	1533
1.95-2.01	54.7	0.907	1579
1.89-1.95	57.3	0.91	1612
1.85-1.89	56.7	0.907	1682
1.8-1.85	60.7	0.893	1687
1.76-1.8	60.8	0.894	1780
1.72-1.76	63.5	0.888	1749
1.68-1.72	63.7	0.891	1838
1.65-1.68	68	0.886	1839
1.61-1.65	67.4	0.867	1916
1.58-1.61	69	0.869	1914
1.55-1.58	71	0.849	1932
1.53-1.55	74.5	0.836	1961
1.5-1.53	75.4	0.764	1860

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing
SHELXL-97		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.5→32.857 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.963 / SU B: 1.989 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18	2049	5.023 %	RANDOM
R_work	0.161	-	-	-
obs	0.162	40794	99.4 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.013 Å²	0 Å²	0 Å²
2-	-	0.122 Å²	0 Å²
3-	-	-	-0.135 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→32.857 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1606	0	49	272	1927

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1741
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.545	1.962	2370
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.586	5	207
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.494	23.81	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.128	15	267
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.371	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	239
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1351
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	780
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	1168
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	202
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	0.266	0.2	41
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.209	0.2	23
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	1.79	3	1048
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.64	5	1671
X-RAY DIFFRACTION	r_scbond_it	4.051	8	800
X-RAY DIFFRACTION	r_scangle_it	5.689	12	696
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.5→1.54 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.288	144	-
R_work	0.24	2695	-
obs	-	-	95.49 %

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	20.5725	6.5442	1.7606	2.5558	2.175	5.6526	-0.0234	0.3435	0.3461	-0.0983	0.1448	0.1978	-0.6986	-0.0753	-0.1214	-0.0212	0.0273	0.0094	-0.1351	0.006	-0.0736	17.2868	30.5622	12.1676
2	1.6548	1.2053	-0.1025	2.5536	0.1986	1.3443	0.006	-0.0014	0.0814	-0.1093	0.01	0.0269	-0.1554	-0.0992	-0.0161	-0.1198	0.0103	0.0002	-0.1043	0.0037	-0.1347	19.159	20.0261	7.3989
3	2.0253	-0.1079	-0.6246	2.4283	0.0882	2.7045	-0.0327	-0.0773	-0.0859	-0.0939	-0.0374	-0.1577	0.1121	0.0763	0.0701	-0.1584	0.0148	-0.0327	-0.1155	-0.0165	-0.1535	23.0373	15.7944	19.5667
4	2.4354	0.1269	-1.0564	1.2684	-0.762	1.9369	0.0913	-0.186	0.2077	0.1494	-0.1028	0.1259	-0.1213	-0.1395	0.0115	-0.11	-0.0047	-0.015	-0.0838	-0.0127	-0.114	15.5354	18.1363	21.3008
5	0.225	-0.2146	-0.2573	3.5058	-1.8182	1.5842	-0.001	-0.1155	0.0234	0.3246	-0.0198	-0.0365	-0.169	0.006	0.0208	-0.1145	-0.0165	-0.0036	-0.0917	-0.0035	-0.1129	17.7916	18.7173	26.8157
6	0.1766	-0.0819	0.3232	1.3954	0.4714	3.5439	0.0097	-0.049	-0.1253	-0.0468	-0.0127	-0.0625	0.0455	0.0597	0.003	-0.1383	0.0294	0.0034	-0.1287	0.0027	-0.1052	26.0563	11.152	11.2026
7	26.7925	-0.851	-5.9702	22.0417	-4.4518	12.894	0.2108	-0.3914	-2.819	-0.1007	-0.3273	0.2097	1.4231	0.0014	0.1165	0.0754	-0.0739	-0.0587	-0.0087	0.0212	0.1563	9.1638	-0.6758	5.8466
8	5.5782	-0.5029	0.847	0.7653	-0.0682	1.0658	0.0064	0.1692	-0.3683	-0.0873	-0.0269	-0.0347	0.1452	0.1142	0.0205	-0.0906	-0.0075	0.0067	-0.0558	-0.0281	-0.1084	20.5751	8.974	2.0155
9	1.2319	0.3163	0.0699	0.7379	1.776	4.7105	0.0413	-0.1678	-0.1034	0.1742	-0.0616	-0.1026	0.2466	0.3262	0.0203	-0.0894	0.0088	-0.0138	-0.0407	0.0308	-0.062	29.7129	11.6612	22.065

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	12 - 18	12 - 18
2	X-RAY DIFFRACTION	2	A	A	19 - 42	19 - 42
3	X-RAY DIFFRACTION	3	A	A	43 - 65	43 - 65
4	X-RAY DIFFRACTION	4	A	A	66 - 92	66 - 92
5	X-RAY DIFFRACTION	5	A	A	93 - 128	93 - 128
6	X-RAY DIFFRACTION	6	A	A	129 - 149	129 - 149
7	X-RAY DIFFRACTION	7	A	A	150 - 157	150 - 157
8	X-RAY DIFFRACTION	8	A	A	158 - 173	158 - 173
9	X-RAY DIFFRACTION	9	A	A	174 - 202	174 - 202

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Protein / Protein/peptide , 2 types, 2 molecules AL

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Non-polymers , 4 types, 283 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi