PDB-2gre: Crystal structure of Deblocking aminopeptidase from Bacillus cereus

ID or keywords:

Entry

Database: PDB / ID: 2gre

Title

Crystal structure of Deblocking aminopeptidase from Bacillus cereus

Components

Deblocking aminopeptidase

Keywords

HYDROLASE / Bacillus cereus Deblocking aminopeptidase / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metal ion binding
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.65 Å

Authors

Chang, C. / Wu, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of Deblocking aminopeptidase from Bacillus cereus
Authors: Chang, C. / Wu, R. / Abdullah, J. / Joachimiak, A.

History

Deposition	Apr 24, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gre.cif.gz	954.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2gre.ent.gz	818.9 KB	Display	PDB format
PDBx/mmJSON format	2gre.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2gre_validation.pdf.gz	615.3 KB	Display	wwPDB validaton report
Full document	2gre_full_validation.pdf.gz	802.7 KB	Display
Data in XML	2gre_validation.xml.gz	195.2 KB	Display
Data in CIF	2gre_validation.cif.gz	265.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/2gre ftp://data.pdbj.org/pub/pdb/validation_reports/gr/2gre	HTTPS FTP

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Related structure data

Similar structure data	2wyr-d 1188 2cf4-1 3kl9-d 1xfo-1 1y0r-1 1y0y-1 2ijz-d 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: APC25341

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Deblocking aminopeptidase

B: Deblocking aminopeptidase

C: Deblocking aminopeptidase

D: Deblocking aminopeptidase

E: Deblocking aminopeptidase

F: Deblocking aminopeptidase

G: Deblocking aminopeptidase

H: Deblocking aminopeptidase

I: Deblocking aminopeptidase

J: Deblocking aminopeptidase

K: Deblocking aminopeptidase

L: Deblocking aminopeptidase

M: Deblocking aminopeptidase

N: Deblocking aminopeptidase

O: Deblocking aminopeptidase

P: Deblocking aminopeptidase

hetero molecules

629 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Deblocking aminopeptidase

B: Deblocking aminopeptidase

C: Deblocking aminopeptidase

D: Deblocking aminopeptidase

E: Deblocking aminopeptidase

F: Deblocking aminopeptidase

G: Deblocking aminopeptidase

H: Deblocking aminopeptidase

I: Deblocking aminopeptidase

J: Deblocking aminopeptidase

K: Deblocking aminopeptidase

L: Deblocking aminopeptidase

hetero molecules

defined by author
472 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

M: Deblocking aminopeptidase

N: Deblocking aminopeptidase

O: Deblocking aminopeptidase

P: Deblocking aminopeptidase

hetero molecules

M: Deblocking aminopeptidase

N: Deblocking aminopeptidase

O: Deblocking aminopeptidase

P: Deblocking aminopeptidase

hetero molecules

M: Deblocking aminopeptidase

N: Deblocking aminopeptidase

O: Deblocking aminopeptidase

P: Deblocking aminopeptidase

hetero molecules

defined by author
472 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	240.918, 240.918, 294.824
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Deblocking aminopeptidase Mass: 39238.875 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) References: GenBank: 29894598, UniProt: Q81HB5*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.62 Å³/Da / Density % sol: 53.09 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.0 M Ammonium sulfate, Na-cacodylate pH6.5, NaCl, 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-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2006
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.55→50 Å / Num. all: 206788 / Num. obs: 206788 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / R_merge(I) obs: 0.095 / Net I/σ(I): 2.64
Reflection shell	Resolution: 2.55→2.64 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.756 / Mean I/σ(I) obs: 2.52 / Num. unique all: 20704 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data scaling
HKL-3000		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.65→50 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.898 / SU B: 25.573 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.788 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26394	9285	5 %	RANDOM
R_work	0.19439	-	-	-
all	0.19789	175594	-	-
obs	0.19789	175594	99.78 %	-

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: 54.235 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.17 Å²	0.09 Å²	0 Å²
2-	-	0.17 Å²	0 Å²
3-	-	-	-0.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	38497	0	80	982	39559

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	39170
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.861	1.959	52963
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.794	5	4833
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.577	24.497	1739
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.846	15	6885
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.579	15	192
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	6125
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	28842
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.266	0.2	20071
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.323	0.2	26488
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.225	0.2	2096
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	0.277	0.2	134
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.23	0.2	21
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	1.116	1.5	24892
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.646	2	39244
X-RAY DIFFRACTION	r_scbond_it	2.369	3	15974
X-RAY DIFFRACTION	r_scangle_it	3.663	4.5	13719
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	713	-
R_work	0.276	12887	-
obs	-	-	99.37 %

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	1.6185	-0.1128	0.0797	1.1379	0.7167	2.4215	-0.1712	0.0275	0.0221	0.042	0.0121	-0.062	-0.1667	0.0552	0.1592	-0.3063	-0.0192	-0.0778	-0.3815	0.0464	-0.3981	106.6977	32.839	104.5369
2	7.242	1.231	0.4197	4.8587	0.7775	9.6753	0.1038	-0.5436	-0.6026	0.2124	0.0611	-0.24	0.6	0.1002	-0.1649	-0.263	-0.0187	-0.0816	-0.2897	0.0854	-0.3709	113.6098	28.82	135.1212
3	1.1678	0.1579	0.6282	2.7516	-0.0076	1.3665	-0.0222	-0.0331	-0.1027	0.1312	0.0337	0.2217	-0.0138	0.102	-0.0115	-0.324	0.0677	0.0423	-0.4513	0.0358	-0.3929	85.1091	15.5747	133.0011
4	3.7974	0.3033	0.6049	8.6017	-0.5335	6.9394	0.0844	0.2633	-0.0732	-0.5893	-0.056	-0.6153	0.3596	0.4424	-0.0284	-0.2393	0.0922	0.035	-0.3863	-0.0149	-0.3393	91.7747	-14.5692	126.507
5	1.5835	0.0828	-0.6754	1.5711	-0.5565	1.388	-0.0156	0.3349	-0.0076	0.0264	-0.0085	-0.0835	0.0619	-0.0462	0.0241	-0.3811	0.0097	-0.0042	-0.298	-0.0581	-0.3169	89.2015	-2.2607	97.7231
6	7.8611	1.0207	-2.4231	6.8919	-0.5289	6.4356	0.0311	-0.5826	0.2772	0.2801	0.0265	-0.5407	0.0197	0.3489	-0.0576	-0.4175	-0.009	-0.0083	-0.275	-0.054	-0.2535	118.7463	7.0884	91.1513
7	0.5943	0.8031	-0.4004	2.9819	-0.249	1.2694	-0.1366	0.2821	-0.1008	-0.0185	0.0953	-0.5734	0.0608	0.3005	0.0413	-0.2902	0.0707	-0.0108	-0.0445	-0.1886	0.1805	166.2652	-28.1397	103.2975
8	5.5505	-0.2795	2.3767	7.0512	-0.4245	5.923	-0.0014	-0.0141	-0.1347	0.0601	0.0659	0.6478	-0.2212	-0.1483	-0.0646	-0.3028	-0.0849	-0.0212	-0.2003	-0.1286	-0.0516	154.482	0.9853	97.6832
9	1.9821	0.7225	-0.0717	3.0544	0.1725	1.3304	-0.1054	0.3565	-0.1937	-0.2989	0.1789	-0.3293	0.0131	0.1914	-0.0735	-0.2759	-0.0272	0.1243	-0.0819	-0.1922	-0.1556	136.6274	-16.7866	78.8618
10	7.5871	-0.4	-1.2257	7.3227	-1.1683	3.7922	-0.2086	-0.8107	-0.205	0.4663	0.0808	-0.1256	0.01	0.4185	0.1277	-0.3242	0.0698	0.0979	-0.3367	-0.1138	-0.2971	112.231	-24.4472	97.6035
11	1.9365	-0.4486	0.6567	1.5501	-0.1628	2.1784	-0.0743	-0.225	0.0177	0.1845	0.0862	-0.0433	0.1742	0.0574	-0.0119	-0.2495	0.0416	0.0587	-0.3884	-0.1671	-0.2612	131.949	-48.2246	102.6533
12	6.5949	0.909	-0.6325	2.7463	0.491	5.5451	-0.2541	-0.2922	0.1549	0.1946	0.1086	0.0065	-0.8714	0.0141	0.1455	-0.0472	0.1426	-0.052	-0.2216	-0.0856	-0.1872	148.9722	-37.8281	127.3072
13	1.8173	0.1678	-0.3627	1.2311	-0.3813	3.1642	0.0543	-0.2815	0.1201	0.2679	-0.128	-0.1662	-0.3884	0.278	0.0737	-0.0915	-0.1941	-0.1539	-0.1643	0.0245	-0.2446	143.0362	39.2776	142.6159
14	6.685	1.1053	0.1943	3.2563	0.6922	9.1956	0.1446	0.2714	-0.6611	0.0923	0.0685	-0.1291	0.6112	0.3643	-0.2132	-0.3509	-0.0977	-0.0716	-0.2743	0.0183	-0.2632	137.5085	29.9102	112.8793
15	1.7248	-0.7177	0.3503	2.2499	0.1283	1.0565	-0.0098	0.052	-0.2385	-0.0511	0.0776	-0.1176	0.088	-0.0019	-0.0677	-0.3386	-0.1636	-0.0142	-0.2777	0.0379	-0.2492	168.2663	23.7127	116.0646
16	3.9506	-0.9078	1.4436	7.86	-0.7593	6.8074	0.0117	-0.0742	-0.5196	0.5042	-0.0213	0.7388	0.2668	-0.1495	0.0095	-0.3458	-0.0655	-0.058	-0.248	0.0487	-0.0158	167.6468	-6.2774	126.6222
17	2.2035	0.4682	-1.4903	1.2616	0.2404	1.9173	-0.0136	-0.4422	-0.1163	0.2713	-0.0135	-0.1592	-0.1614	0.363	0.027	-0.1769	-0.0901	-0.1722	0.0782	0.1905	-0.1039	167.8271	9.8022	153.5403
18	5.9737	0.5805	-1.6606	6.1547	-2.4121	6.2247	-0.0623	0.6377	0.1548	-0.1784	0.0956	0.3687	0.0094	-0.1842	-0.0333	-0.1687	-0.0741	-0.0316	-0.1248	0.1551	-0.232	136.6486	13.6148	159.3432
19	0.9778	-0.3948	0.0735	3.4349	0.4751	2.6311	-0.1038	-0.1366	-0.2311	0.3535	-0.0242	0.1435	0.4203	-0.0119	0.128	0.0057	0.0569	0.1283	-0.3325	0.1046	-0.251	97.6162	-31.9523	153.163
20	3.6391	0.419	0.8478	7.82	-0.2181	6.1293	-0.0762	0.3982	0.1383	0.0015	-0.0868	-0.9176	-0.1603	0.4719	0.163	-0.1967	0.0341	0.0131	-0.3378	0.094	-0.4214	103.0615	-0.6754	153.9407
21	2.6027	-0.2283	0.1093	1.151	-0.1881	1.0893	0.0723	0.0009	-0.0037	-0.0151	-0.142	-0.1769	-0.0654	0.2766	0.0697	-0.1144	0.02	0.0354	-0.2515	0.0873	-0.4459	123.8446	-11.4536	175.0967
22	7.9862	-0.2936	-1.7571	6.0481	1.0359	3.5591	-0.1527	0.9468	-0.0187	-0.2824	0.0305	-0.1945	0.1283	-0.1252	0.1222	-0.184	0.0642	0.0126	0.0089	0.1513	-0.3287	149.4947	-16.2941	156.914
23	1.251	0.6647	0.4736	1.3062	0.6393	2.2348	0.0502	-0.0073	-0.3196	0.1793	-0.0601	0.0404	0.465	0.2568	0.0099	0.117	0.2626	0.0228	-0.1093	0.1069	-0.1658	135.5271	-44.1499	155.7272
24	8.0704	-0.8116	0.0806	4.3703	3.0478	7.7587	-0.3175	0.2287	0.2159	0.0799	0.1409	0.1256	-0.4991	-0.4253	0.1766	-0.0744	0.1234	0.0508	-0.2238	-0.0336	-0.2471	116.8082	-41.2647	130.045
25	1.9996	0.5733	-0.5934	2.9606	0.2115	2.2941	-0.0797	0.2631	-0.2855	-0.16	0.1611	-0.452	0.0815	0.2911	-0.0815	-0.1353	0.0403	0.0976	0.0834	-0.204	0.1031	45.399	-18.803	116.1121
26	5.3905	0.1338	-1.8927	7.8417	0.4407	7.3289	0.2714	0.2912	0.1038	-0.3967	-0.1401	0.3648	-0.3975	-0.4613	-0.1313	-0.1988	0.0155	0.097	-0.0641	-0.0326	-0.1527	34.5998	9.207	126.2586
27	0.8707	-0.6532	-0.6477	2.9713	0.2656	2.0985	-0.0625	0.0591	0.0654	0.0543	0.1548	-0.0982	0.1355	0.1537	-0.0923	-0.1948	-0.0087	-0.0099	-0.139	-0.1031	-0.2149	21.7828	7.6653	155.6245
28	7.9889	0.0359	-1.3854	10.3469	0.5848	6.3172	-0.0855	0.5279	-0.1815	-0.3643	-0.0511	0.3861	0.2812	-0.4603	0.1366	-0.1245	-0.0413	0.0211	-0.0932	-0.1233	-0.1737	21.669	-18.6209	138.0116
29	3.0356	-0.093	0.9269	1.8898	0.106	0.6956	0.1367	0.3345	0.4287	-0.1688	-0.0102	-0.0796	-0.2867	0.281	-0.1264	0.2004	0.1379	0.1259	0.3504	0.2267	0.0608	-1.4667	36.1898	78.7217
30	8.2807	-0.3241	-0.2871	5.049	1.6483	7.45	-0.0872	-0.564	-0.0965	0.3202	0.2682	-0.0058	-0.1096	-0.3261	-0.181	-0.0396	0.1172	0.1246	0.1173	0.0775	0.0493	17.8673	33.3361	103.7567
31	1.772	-0.2599	0.344	0.9601	-0.3849	2.6533	0.0234	0.2988	0.1797	-0.0416	-0.0595	0.0771	-0.0394	-0.2171	0.0361	-0.214	-0.0474	0.1185	-0.0248	-0.0386	-0.0249	44.3428	16.1721	97.3032
32	4.9149	-0.2879	1.8861	5.9009	1.1463	7.1335	0.1702	-0.1842	-0.3955	-0.2494	0.0839	0.4394	0.102	-0.7513	-0.2541	-0.0861	-0.0083	0.0661	0.2881	0.0388	0.0107	18.2289	11.0151	79.8258

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	4 - 73	4 - 73
2	X-RAY DIFFRACTION	1	A	A	168 - 348	168 - 348
3	X-RAY DIFFRACTION	2	A	A	74 - 167	74 - 167
4	X-RAY DIFFRACTION	3	B	B	4 - 73	4 - 73
5	X-RAY DIFFRACTION	3	B	B	168 - 348	168 - 348
6	X-RAY DIFFRACTION	4	B	B	74 - 167	74 - 167
7	X-RAY DIFFRACTION	5	C	C	4 - 73	4 - 73
8	X-RAY DIFFRACTION	5	C	C	168 - 348	168 - 348
9	X-RAY DIFFRACTION	6	C	C	74 - 167	74 - 167
10	X-RAY DIFFRACTION	7	D	D	4 - 73	4 - 73
11	X-RAY DIFFRACTION	7	D	D	168 - 348	168 - 348
12	X-RAY DIFFRACTION	8	D	D	74 - 167	74 - 167
13	X-RAY DIFFRACTION	9	E	E	4 - 73	4 - 73
14	X-RAY DIFFRACTION	9	E	E	168 - 348	168 - 348
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