PDB-3ngf: Crystal structure of AP endonuclease, family 2 from Brucella meli...

ID or keywords:

Entry

Database: PDB / ID: 3ngf

Title

Crystal structure of AP endonuclease, family 2 from Brucella melitensis

Components

AP endonuclease, family 2

Keywords

ISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TIM Barrel / AP Nuclease

Function / homology

Function and homology information

hydroxypyruvate isomerase / hydroxypyruvate isomerase activity / endonuclease activity / metal ion binding
Similarity search - Function

Biological species

Brucella melitensis biovar Abortus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of AP endonuclease, family 2 from Brucella melitensis
Authors: Staker, B. / Edwards, T. / Bullen, J. / Dieterich, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Jun 11, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 7, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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	3ngf.cif.gz	246.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3ngf.ent.gz	200.4 KB	Display	PDB format
PDBx/mmJSON format	3ngf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ngf_validation.pdf.gz	437.7 KB	Display	wwPDB validaton report
Full document	3ngf_full_validation.pdf.gz	438.9 KB	Display
Data in XML	3ngf_validation.xml.gz	26.4 KB	Display
Data in CIF	3ngf_validation.cif.gz	40.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngf ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngf	HTTPS FTP

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Related structure data

Related structure data	1k77S S: Starting model for refinement
Similar structure data	5t9b-d 2zvr-2 1psr-d 1k77-d 2q17-3 4ee6-1 5y7c-1 3efr-1 1m9h-d 1sv6-3 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
Other databases	TargetDB: BrabA.00070.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: AP endonuclease, family 2

B: AP endonuclease, family 2

hetero molecules

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

1

A: AP endonuclease, family 2

hetero molecules

defined by author&software
30.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AP endonuclease, family 2

hetero molecules

defined by author&software
30.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.980, 120.640, 54.680
Angle α, β, γ (deg.)	90.00, 117.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	AP endonuclease, family 2 Mass: 30467.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria) Strain: 2308 / Gene: BAB2_0144 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YLA2, hydroxypyruvate isomerase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.55 Å³/Da / Density % sol: 51.8 %
Crystal grow	Method: vapor diffusion, sitting drop Details: 0.04 M KH2PO4, 16% PEG 8000, 20% GLYCEROL, 27 MG/ML PROTEIN, JCSG+ SCREEN WELL D12, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 11, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.8→45.91 Å / Num. obs: 55966 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 22.44 Å² / R_merge(I) obs: 0.045 / Net I/σ(I): 14.46
Reflection shell	Resolution: 1.8→1.85 Å / Mean I/σ(I) obs: 3.6 / % possible all: 93.6

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Processing

Software

Name	Version	Classification
StructureStudio		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1K77

1k77

Resolution: 1.8→50.01 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / SU B: 4.379 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	2836	5.1 %	RANDOM
R_work	0.141	-	-	-
obs	0.143	55914	-	-

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: 13.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.19 Å²	0 Å²	6.95 Å²
2-	-	0.34 Å²	0 Å²
3-	-	-	-4.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→50.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4120	0	38	595	4753

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	4417
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3012
X-RAY DIFFRACTION	r_angle_refined_deg	1.315	1.95	6006
X-RAY DIFFRACTION	r_angle_other_deg	0.916	3	7272
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.538	5	550
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.201	23.476	233
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.894	15	693
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.288	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	621
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	5096
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	980
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	0.637	1.5	2678
X-RAY DIFFRACTION	r_mcbond_other	0.2	1.5	1080
X-RAY DIFFRACTION	r_mcangle_it	1.078	2	4311
X-RAY DIFFRACTION	r_scbond_it	1.847	3	1739
X-RAY DIFFRACTION	r_scangle_it	2.868	4.5	1695
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.255	203	-
R_work	0.225	3649	-
obs	-	-	92.22 %

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	0.673	0.4991	-0.5931	2.1257	-1.2859	3.052	-0.0365	0.0817	-0.0063	-0.1602	0.0963	0.0744	0.124	-0.1424	-0.0598	0.0409	-0.0274	-0.0384	0.0148	0.0102	0.0663	-34.637	1.5196	-6.9346
2	2.212	-1.5985	1.8986	2.6119	-2.2572	1.7738	0.0475	0.2333	0.048	0.0624	-0.1439	0.0017	-0.1005	0.2461	0.0964	0.0842	-0.0244	-0.0102	0.1359	0.0024	0.0828	-24.0656	10.4953	-7.4742
3	1.4943	-0.2531	0.2541	0.3109	-0.4783	1.7227	-0.0228	-0.0147	0.0402	-0.0494	0.0705	0.0389	-0.0481	-0.0186	-0.0477	0.0644	-0.0276	-0.0232	0.0408	-0.0024	0.0864	-28.0507	7.5105	-2.9845
4	1.5714	0.0088	0.2252	1.1423	-0.4559	1.1288	-0.0118	0.0104	0.0245	-0.0521	0.0135	-0.1093	-0.043	0.2101	-0.0018	0.0165	-0.0113	-0.0123	0.0685	-0.014	0.0406	-15.7094	7.0915	4.3957
5	3.6598	-1.334	-0.3031	5.1156	0.8	2.654	0.0216	-0.1699	-0.0808	0.2975	-0.0206	-0.3549	0.1339	0.4075	-0.001	0.0192	0.0088	-0.0521	0.1487	0.0095	0.0823	-9.979	1.1566	15.1811
6	0.6137	0.0727	-0.2186	2.6955	0.4162	1.1188	-0.047	-0.0181	-0.0294	-0.052	0.0973	-0.1884	0.0411	0.1293	-0.0503	0.0273	0.0009	-0.0156	0.0315	-0.0032	0.0681	-20.048	0.1042	9.3176
7	1.5106	1.2007	0.2046	4.4683	1.0914	2.1111	0.0477	-0.104	-0.135	0.294	-0.0272	-0.127	0.1832	0.1489	-0.0205	0.0506	0.0145	-0.0297	0.0674	0.0101	0.0609	-19.9967	-2.2903	19.9281
8	0.2552	0.4683	-0.0073	2.6666	0.2926	0.2234	0.0001	-0.0661	-0.0306	0.1171	-0.0244	0.0919	0.0966	0.0599	0.0242	0.0823	-0.0004	-0.0066	0.0237	0.0075	0.0984	-28.4994	-6.811	14.7323
9	1.098	0.7691	0.3131	1.3511	0.6242	2.1785	-0.0634	-0.0006	0.0237	-0.0416	0.0097	0.1344	0.1446	-0.0929	0.0538	0.0811	-0.0056	-0.0107	-0.0006	0.0197	0.0843	-32.0555	-7.8427	5.8734
10	1.0377	0.1437	-0.0123	4.08	0.3395	2.1386	-0.0135	0.0414	0.1237	0.1135	-0.0109	0.4211	0.1132	-0.1409	0.0244	0.0571	-0.0217	-0.0036	0.0051	0.0263	0.1376	-39.8754	-10.6913	9.9127
11	1.1148	-0.3566	-0.9614	3.4151	1.9204	5.3999	-0.0684	0.0042	0.0106	0.0506	0.038	0.181	0.1717	-0.2216	0.0304	0.0494	-0.0191	-0.0221	0.0092	0.0099	0.0821	-35.3566	-3.784	2.6896
12	8.1054	0.1956	-3.3553	3.0638	1.1953	7.471	-0.0638	0.0326	0.0741	-0.447	0.1465	0.5325	0.1626	-0.6254	-0.0827	0.0592	-0.0689	-0.0924	0.0673	0.0536	0.1353	-43.1517	-5.816	-4.5486
13	1.7148	0.5594	-0.9262	2.2525	-0.7624	2.2416	0.0388	0.0386	0.0925	0.0214	0.0509	0.1973	-0.0543	-0.1116	-0.0897	0.0307	0.0193	-0.0317	0.0222	0.027	0.1014	-48.8797	-37.3983	21.2489
14	3.4553	1.9454	0.5168	3.1631	0.0154	-0.1919	0.0418	-0.4494	-0.0381	0.09	-0.1505	-0.0199	0.0611	-0.0165	0.1087	0.092	0.0162	-0.0021	0.1486	0.0251	0.1012	-43.194	-46.07	31.2469
15	3.4369	1.2423	0.717	1.0142	0.3622	1.614	-0.0439	0.0498	-0.0235	-0.0081	0.0587	0.084	0.084	0.0034	-0.0148	0.0494	0.0232	-0.0193	0.0232	0.0135	0.0702	-41.9644	-43.3735	24.9493
16	1.8074	0.4136	0.347	1.4708	-0.2454	1.0899	-0.0427	-0.1925	0.0067	0.1215	0.0512	-0.0471	-0.0317	0.085	-0.0086	0.0237	0.0252	-0.0155	0.0562	-0.0097	0.0314	-28.1892	-41.8197	30.8802
17	2.3085	0.1548	0.5871	5.4849	2.2518	2.3391	0.0163	-0.0818	0.1115	0.1124	0.1015	-0.4874	-0.0179	0.3637	-0.1178	0.0168	-0.002	-0.039	0.1351	-0.0227	0.0931	-16.4525	-38.1119	27.8615
18	0.526	-0.7283	-0.3023	5.6291	0.7437	1.1263	-0.0716	-0.0575	0.0043	0.2541	0.0864	0.0414	0.0506	0.0686	-0.0149	0.0348	0.0006	-0.0155	0.029	-0.0045	0.0655	-28.2201	-38.3298	23.0116
19	1.7926	-0.8482	-0.0593	1.8319	-0.3616	1.1548	0.0772	0.0105	0.2062	-0.057	-0.0485	-0.2759	-0.1824	0.1376	-0.0287	0.0539	-0.0173	-0.0189	0.0469	-0.015	0.1091	-20.6201	-31.4628	21.2148
20	0.3614	-0.3451	-0.0125	1.9503	0.0845	0.1385	0.0296	0.0141	0.0833	-0.0419	-0.0087	-0.0369	-0.0723	0.0968	-0.0208	0.0937	-0.0053	-0.0131	0.0434	0.006	0.0949	-28.3626	-28.917	14.5107
21	2.6583	-1.4013	-0.6852	2.01	0.1228	0.7666	0.1064	0.0951	0.0658	-0.0795	-0.0201	0.0637	-0.0657	-0.0212	-0.0863	0.0789	-0.0098	-0.0149	-0.0011	0.012	0.0724	-35.7928	-28.1668	15.4853
22	1.3898	-0.7812	-0.4282	3.8531	-0.4707	0.2313	0.0668	0.1126	-0.0123	-0.3664	-0.0063	0.1308	0.062	-0.075	-0.0605	0.1145	-0.0047	-0.0251	0.017	0.0142	0.0875	-38.0745	-26.4213	7.4952
23	3.1682	-1.3216	-1.1981	3.0615	0.9425	2.7748	0.0233	0.0754	0.1519	-0.0582	0.1258	0.1483	-0.1174	-0.162	-0.1491	0.0545	-0.0011	-0.0198	0.0152	0.048	0.1162	-46.3641	-30.5133	17.8915
24	19.5751	-0.7298	-2.61	3.353	-0.4183	20.516	0.1686	0.8837	-0.2062	-0.3656	-0.055	0.4631	0.5083	0.0512	-0.1136	0.0674	-0.0075	-0.0902	0.0841	0.0552	0.1154	-50.6412	-31.1775	10.1108

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 34
2	X-RAY DIFFRACTION	2	A	35 - 47
3	X-RAY DIFFRACTION	3	A	48 - 66
4	X-RAY DIFFRACTION	4	A	67 - 109
5	X-RAY DIFFRACTION	5	A	110 - 128
6	X-RAY DIFFRACTION	6	A	129 - 155
7	X-RAY DIFFRACTION	7	A	156 - 168
8	X-RAY DIFFRACTION	8	A	169 - 195
9	X-RAY DIFFRACTION	9	A	196 - 213
10	X-RAY DIFFRACTION	10	A	214 - 230
11	X-RAY DIFFRACTION	11	A	231 - 244
12	X-RAY DIFFRACTION	12	A	245 - 257
13	X-RAY DIFFRACTION	13	B	0 - 34
14	X-RAY DIFFRACTION	14	B	35 - 47
15	X-RAY DIFFRACTION	15	B	48 - 66
16	X-RAY DIFFRACTION	16	B	67 - 112
17	X-RAY DIFFRACTION	17	B	113 - 128
18	X-RAY DIFFRACTION	18	B	129 - 149
19	X-RAY DIFFRACTION	19	B	150 - 168
20	X-RAY DIFFRACTION	20	B	169 - 193
21	X-RAY DIFFRACTION	21	B	194 - 213
22	X-RAY DIFFRACTION	22	B	214 - 232
23	X-RAY DIFFRACTION	23	B	233 - 249
24	X-RAY DIFFRACTION	24	B	250 - 257

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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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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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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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi