PDB-3l2m: X-ray Crystallographic Analysis of Pig Pancreatic Alpha-Amylase w...

ID or keywords:

Entry

Database: PDB / ID: 3l2m

Title

X-ray Crystallographic Analysis of Pig Pancreatic Alpha-Amylase with Alpha-cyclodextrin

Components

Pancreatic alpha-amylase

Keywords

HYDROLASE /

catalytic domain / carbohydrate binding module /

alpha-cyclodextrin /

Carbohydrate metabolism /

Glycoprotein / Glycosidase / Metal-binding /

Pyrrolidone carboxylic acid /

Secreted

Function / homology

Function and homology information

alpha-amylase / carbohydrate catabolic process /

alpha-amylase activity /

chloride ion binding / carbohydrate metabolic process /

calcium ion binding /

extracellular space
Similarity search - Function

Biological species

Sus scrofa (pig)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Larson, S.B. / Day, J.S. / McPherson, A.

Citation

Journal: Biochemistry / Year: 2010
Title: X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.
Authors: Larson, S.B. / Day, J.S. / McPherson, A.

History

Deposition	Dec 15, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software Item: _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 ..._pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.0	Dec 25, 2019	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l2m.cif.gz	223.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3l2m.ent.gz	188.2 KB	Display	PDB format
PDBx/mmJSON format	3l2m.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/l2/3l2m ftp://data.pdbj.org/pub/pdb/validation_reports/l2/3l2m	HTTPS FTP

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Related structure data

Related structure data	3l2lC C: citing same article (ref.)
Similar structure data	5td4-d 2cpu-d 1b2y-d 3ij7-d 1xu7-2 1xd0-d 6obx-d 1ose-d 3czr-d 3bai-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (10) #138 - Jun 2011 Glucansucrase similarity (9)

Deposited unit

A: Pancreatic alpha-amylase

hetero molecules

58.5 kDa, 1 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)	70.650, 114.880, 118.850
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Pancreatic alpha-amylase / PA / 1 / 4-alpha-D-glucan glucanohydrolase

Mass: 55439.781 Da / Num. of mol.: 1 / Fragment: residues 16-511 / Source method: isolated from a natural source / Details: pancreas / Source: (natural)

Sus scrofa (pig) / References: UniProt: P00690,

alpha-amylase

#2: Polysaccharide

Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin /

Α-Cyclodextrin

Type: oligosaccharide

, Oligosaccharide

/ Class: Drug delivery

/ Mass: 990.860 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References:

alpha-cyclodextrin

#3: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

#4: Chemical

ChemComp-CL / CHLORIDE ION /

Chloride

Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H₂O

Sequence details

THE RESIDUE AT POSITION 426 IS A VARIANT AS LISTED IN UNP ENTRY P00690.PCA IS A POST-TRANSLATIONAL ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.35 Å³/Da / Density % sol: 71.72 %
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 6.75 Details: 0.010 M cacodylate, 0.002 M calcium chloride, soaking of alpha-cyclodextrin, pH 6.75, EVAPORATION, temperature 298K

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Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: SDMS / Detector: AREA DETECTOR / Date: Jun 17, 1993
Radiation	Monochromator: Supper graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.97→29.3 Å / Num. all: 62592 / Num. obs: 62592 / % possible obs: 84.6 % / Redundancy: 4.84 % / B_iso Wilson estimate: 22 Å² / Limit h max: 35 / Limit h min: 0 / Limit k max: 58 / Limit k min: 0 / Limit l max: 60 / Limit l min: 0 / R_merge(I) obs: 0.068 / Net I/σ(I): 19.83
Reflection shell	Resolution: 1.97→2.07 Å / Redundancy: 1.61 % / R_merge(I) obs: 0.178 / Mean I/σ(I) obs: 3.07 / Num. unique all: 5276 / % possible all: 36.6

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Processing

Software

Name	Version	Classification
SDMS	Detector System	data collection
REFMAC	5.5.0089	refinement
SDMS	Detector System	data reduction
SDMS	Detector System	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→29.3 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.955 / Num. parameters: 20617 / Num. restraintsaints: 33259 / WR_factor R_free: 0.1351 / WR_factor R_work: 0.1038 / Occupancy max: 1 / SU B: 5.189 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1008 / SU R_free: 0.1019 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16021	6279	10.1 %	RANDOM
R_work	0.12666	-	-	-
all	0.13005	55805	-	-
obs	0.13005	55805	89.25 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 18.81 Å²

	B_aniso -1	B_aniso -2
1-	0.49 Å²	0 Å²
2-	-	-0.48 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.97→29.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3909	0	200	592	4701

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	4613
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4234
X-RAY DIFFRACTION	r_angle_refined_deg	1.387	1.973	6371
X-RAY DIFFRACTION	r_angle_other_deg	0.712	3	9569
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.89	5	587
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.692	23.964	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.896	15	702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.079	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	702
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5208
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1127
X-RAY DIFFRACTION	r_mcbond_it	2.148	4	2671
X-RAY DIFFRACTION	r_mcbond_other	0.551	4	1097
X-RAY DIFFRACTION	r_mcangle_it	3.128	8	4352
X-RAY DIFFRACTION	r_scbond_it	3.789	8	1942
X-RAY DIFFRACTION	r_scangle_it	4.917	10	1995
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	1.794	15	2
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.3	878
X-RAY DIFFRACTION	r_nbd_other	0.183	0.3	4002
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.5	2268
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.5	2666
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.204	0.5	673
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.18	0.5	507
X-RAY DIFFRACTION	r_metal_ion_refined	0.016	0.5	2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.131	0.3	9
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.221	0.3	34
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.199	0.5	33
X-RAY DIFFRACTION	r_symmetry_hbond_other	0.192	0.5	10
X-RAY DIFFRACTION	r_mcangle_other	1.799	8	3698
X-RAY DIFFRACTION	r_scbond_other	1.343	8	3137
X-RAY DIFFRACTION	r_scangle_other	2.392	10	5871

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
1.97-2.016	0.279	103	0.24	1115	1115	23.96
2.016-2.071	0.21	361	0.195		3363	75.89
2.071-2.131	0.2	434	0.177		3613	84.21
2.131-2.196	0.223	413	0.164		3604	85.93
2.196-2.267	0.171	412	0.152		3653	89.97
2.267-2.346	0.191	413	0.148		3877	98.01
2.346-2.434	0.177	441	0.137		3782	98.95
2.434-2.533	0.182	400	0.132		3643	99.07
2.533-2.645	0.161	407	0.122		3509	99.85
2.645-2.773	0.163	400	0.124		3344	99.95
2.773-2.921	0.164	372	0.113		3194	100
2.921-3.097	0.15	296	0.114		3126	99.94
3.097-3.308	0.139	344	0.108		2859	99.97
3.308-3.569	0.135	298	0.107		2691	99.97
3.569-3.904	0.125	283	0.095		2485	100
3.904-4.355	0.112	272	0.088		2255	100
4.355-5.01	0.112	229	0.089		2031	99.74
5.01-6.092	0.146	188	0.112		1694	98.02
6.092-8.435	0.183	128	0.143		1249	89.13
8.435-29.298	0.311	85	0.299		718	82.96

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	0.835	0.188	0.0898	1.7747	0.1977	0.8629	0.0143	-0.0026	-0.014	-0.0034	-0.0153	-0.0699	-0.0073	0.0197	0.0011	0.0006	0.0021	0.0001	0.0188	0.0026	0.0031	38.931	33.386	44.709
2	5.155	0.9228	-0.47	1.7747	0.1809	1.4466	0.1441	-0.4025	0.1741	0.2686	-0.0905	0.0382	-0.1302	-0.0224	-0.0536	0.0975	-0.0004	-0.0053	0.0623	-0.0163	0.0144	35.074	49.807	62.128
3	2.4994	0.1172	-0.4477	2.384	0.1431	3.1792	-0.0087	0.1004	-0.1004	-0.1249	0.0105	-0.0574	0.1369	0.036	-0.0019	0.0252	0.0054	0.0018	0.0174	-0.0181	0.0213	32.511	9.098	28.89
4	13.4249	-2.1124	4.4645	0.3327	-0.7024	1.4847	-0.0772	-0.0514	0.2232	0.0101	0.0031	-0.0356	-0.024	-0.0191	0.074	0.1321	0.0115	0.0083	0.094	0.0007	0.0856	51.594	39.179	73.09
5	14.4903	9.5915	5.688	17.3134	8.3356	4.1381	0.0925	-0.0313	-0.1038	0.0312	-0.225	0.3434	0.0241	-0.095	0.1325	0.1232	0.048	0.0271	0.1786	0.0305	0.0924	48.269	42.572	72.46
6	2.5206	-8.3057	-0.0592	30.2411	6.714	14.8188	-0.1006	-0.0301	0.0256	0.206	-0.044	0.0035	-0.2935	-0.322	0.1445	0.1049	-0.019	-0.0029	0.1771	-0.0149	0.1324	43.648	41.504	71.405
7	16.6495	-8.778	-2.3074	4.6282	1.2162	0.3205	0.0639	0.2091	-0.247	-0.0329	-0.1043	0.1313	-0.0102	-0.0398	0.0403	0.1329	-0.0034	-0.0002	0.1842	-0.0394	0.154	42.298	37.128	71.037
8	9.514	15.1784	1.5142	26.7351	5.6974	4.5194	-0.1346	-0.0478	0.1167	0.0154	-0.0699	0.347	0.2749	-0.0032	0.2044	0.1048	0.0078	0.0023	0.1416	0.0161	0.1314	45.624	33.118	71.917
9	1.5975	-6.4172	0	26.5439	0	21.9417	0.0687	0.0051	-0.0581	-0.275	-0.0698	0.2806	0.2261	-0.128	0.0012	0.0711	-0.0202	-0.0026	0.1303	-0.0145	0.1079	50.123	34.226	72.924
10	39.5054	-0.0265	20.1669	0.0001	-0.0135	10.295	-0.1399	-0.3446	0.2656	0.0032	0.0022	-0.0012	-0.0703	-0.1739	0.1377	0.2816	-0.0079	0.0417	0.1343	-0.0284	0.1517	39.085	37.042	64.292
11	32.1507	0	2.3708	0.2808	0	20.0226	-0.1663	-0.1439	-0.2042	0.017	0.0157	0.018	0.1077	0.1051	0.1505	0.2857	-0.0043	-0.0637	0.1603	0.0169	0.2374	37.166	35.162	59.819
12	0.533	1.8822	4.9604	6.6498	17.5254	46.188	0.0087	0.0517	-0.0245	0.0096	0.1804	-0.0747	0.0305	0.4743	-0.1891	0.1655	0.013	0.045	0.1445	0.0344	0.2598	32.46	35.07	59.875
13	23.1035	2.1751	10.1743	0.205	0.958	4.4811	0.0834	0.4098	-0.2888	0.0098	0.0429	-0.0281	0.0485	0.1816	-0.1264	0.2673	0.0089	0.0299	0.1372	0.014	0.1372	29.747	36.024	64.105
14	37.0412	0	6.3629	1.8099	0	22.3709	0.0313	-0.1018	0.0721	-0.011	0.0237	-0.0154	-0.0237	0.0779	-0.0549	0.2353	-0.0212	-0.109	0.1142	0.0094	0.2278	31.617	37.32	68.3
15	0.7482	1.3991	4.3872	2.6166	8.205	25.7302	0.0607	-0.0777	0.012	0.107	-0.1479	0.0276	0.3432	-0.4737	0.0871	0.1352	0.0178	0.0445	0.1804	0.0258	0.2634	36.598	38.138	68.57
16	27.6998	0	0.0011	7.9803	-0.0018	0.1246	-0.1279	0.313	0.1873	0.0736	-0.0458	-0.1254	-0.0669	0.0419	0.1737	0.2345	-0.0438	0.0614	0.3217	-0.061	0.3201	40.055	66.841	64.017
17	2.5677	5.3433	8.2033	11.1202	17.0723	26.2104	-0.0001	0.1029	-0.0724	-0.0023	0.2122	-0.1407	-0.0052	0.3244	-0.212	0.1613	0.0364	0.0011	0.1935	0.0707	0.2345	36.34	69.875	63.533
18	25.9793	0	0	52.1359	0	53.1797	-0.4829	0.6259	0.5448	0.178	0.1689	-0.5684	0.2388	-0.6138	0.314	0.1374	-0.0033	0.0062	0.1587	0.0017	0.1366	33.021	69.485	59.435
19	42.1025	-5.0266	16.0084	0.6003	-1.9111	6.087	-0.0682	-0.0331	0.1688	0.0039	0.0038	-0.0185	-0.0317	-0.0167	0.0643	0.2336	0.0155	0.0571	0.1592	-0.0191	0.1868	34.735	65.757	56.366
20	0.0261	1.0459	0.5815	43.0648	23.9271	13.296	-0.0013	0.0071	-0.0047	0.0856	-0.0274	0.0484	0.0328	-0.0175	0.0287	0.1174	0.0029	0.0086	0.1995	0.0388	0.218	39.476	63.952	56.299
21	43.1989	-0.6859	-0.0021	27.0931	0.0007	0.1641	-0.495	-0.026	-0.5081	0.0169	0.3641	0.317	0.1812	-0.055	0.131	0.3064	-0.0287	0.0149	0.1688	-0.0234	0.2006	42.608	65.519	59.651

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 99
2	X-RAY DIFFRACTION	1	A	169 - 403
3	X-RAY DIFFRACTION	2	A	100 - 168
4	X-RAY DIFFRACTION	3	A	404 - 496
5	X-RAY DIFFRACTION	4	A	601
6	X-RAY DIFFRACTION	5	A	602
7	X-RAY DIFFRACTION	6	A	603
8	X-RAY DIFFRACTION	7	A	604
9	X-RAY DIFFRACTION	8	A	605
10	X-RAY DIFFRACTION	9	A	606
11	X-RAY DIFFRACTION	10	A	701
12	X-RAY DIFFRACTION	11	A	702
13	X-RAY DIFFRACTION	12	A	703
14	X-RAY DIFFRACTION	13	A	704
15	X-RAY DIFFRACTION	14	A	705
16	X-RAY DIFFRACTION	15	A	706
17	X-RAY DIFFRACTION	16	A	801
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19	X-RAY DIFFRACTION	18	A	803
20	X-RAY DIFFRACTION	19	A	804
21	X-RAY DIFFRACTION	20	A	805
22	X-RAY DIFFRACTION	21	A	806

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