PDB-5kz6: 1.25 Angstrom Crystal Structure of Chitinase from Bacillus anthracis.

ID or keywords:

Entry

Database: PDB / ID: 5kz6

Title

1.25 Angstrom Crystal Structure of Chitinase from Bacillus anthracis.

Components

Chitinase

Keywords

HYDROLASE / Chitinase / TIM barrel / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

chitinase / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.252 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.25 Angstrom Crystal Structure of Chitinase from Bacillus anthracis.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jul 22, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2016	Group: Data collection
Revision 1.2	Oct 4, 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 / pdbx_struct_oper_list / struct_conn 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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kz6.cif.gz	340.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5kz6.ent.gz	277.8 KB	Display	PDB format
PDBx/mmJSON format	5kz6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kz6_validation.pdf.gz	429.5 KB	Display	wwPDB validaton report
Full document	5kz6_full_validation.pdf.gz	430.8 KB	Display
Data in XML	5kz6_validation.xml.gz	37.4 KB	Display
Data in CIF	5kz6_validation.cif.gz	61.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kz/5kz6 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/5kz6	HTTPS FTP

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Related structure data

Related structure data	3n11S S: Starting model for refinement
Similar structure data	4ysa-d 1jtf-d 3hp7-d 5jgw-4 6l46-d 4tq4-3 1u5r-2 3wkp-d 4zk8-d 2qiy-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chitinase

B: Chitinase

hetero molecules

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

1

A: Chitinase

hetero molecules

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

2

B: Chitinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.243, 94.147, 243.571
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-401- ZN
2	1	A-1011- HOH
3	1	B-939- HOH

#1: Protein	Chitinase / Extracellular exochitinase Chi36 Mass: 36770.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: chi36, GBAA_3854, ADK18_18580 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q81WW1, UniProt: A0A6L7H1P2*PLUS
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1091 / 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: 2.09 Å³/Da / Density % sol: 41.3 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein: 16.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: PACT (B12), 0.01M Zinc chloride, 0.1M MES (pH 6.0), 20% (w/v) PEG6000. Cryo: 4M Sodium formate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2016 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.25→30 Å / Num. obs: 174224 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / B_iso Wilson estimate: 12.5 Å² / R_merge(I) obs: 0.063 / R_sym value: 0.063 / Net I/σ(I): 28.2
Reflection shell	Resolution: 1.25→1.27 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.552 / Mean I/σ(I) obs: 3.2 / CC_1/2: 0.852 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3N11

3n11

Resolution: 1.252→28.1 Å / Cor.coef. F_o:F_c: 0.982 / Cor.coef. F_o:F_c free: 0.978 / SU B: 1.084 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.13952	8767	5 %	RANDOM
R_work	0.11743	-	-	-
obs	0.11852	165370	99.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 15.559 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0 Å²	0 Å²
2-	-	0.18 Å²	0 Å²
3-	-	-	-0.25 Å²

Refinement step

Cycle: 1 / Resolution: 1.252→28.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5062	0	9	1091	6162

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	5871
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	5410
X-RAY DIFFRACTION	r_angle_refined_deg	1.337	1.952	8050
X-RAY DIFFRACTION	r_angle_other_deg	0.867	3	12550
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.367	5	791
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.757	24.806	258
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.144	15	969
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.577	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	824
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.021	7122
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	1406
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	0.745	0.944	2981
X-RAY DIFFRACTION	r_mcbond_other	0.745	6.175	2980
X-RAY DIFFRACTION	r_mcangle_it	1.034	1.424	3833
X-RAY DIFFRACTION	r_mcangle_other	1.034		3834
X-RAY DIFFRACTION	r_scbond_it	1.065	1.087	2890
X-RAY DIFFRACTION	r_scbond_other	1.064		2891
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.318	1.573	4218
X-RAY DIFFRACTION	r_long_range_B_refined	2.575		7312
X-RAY DIFFRACTION	r_long_range_B_other	1.887		6928
X-RAY DIFFRACTION	r_rigid_bond_restr	1.422	3	5871
X-RAY DIFFRACTION	r_sphericity_free	19.126	5	697
X-RAY DIFFRACTION	r_sphericity_bonded	7.078	5	6051

LS refinement shell

Resolution: 1.252→1.284 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.219	611	-
R_work	0.204	12094	-
obs	-	-	99.62 %

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	1.4716	-0.1828	-1.558	0.8099	0.3018	2.6935	0.0558	0.0501	0.1339	-0.1158	-0.0017	-0.0031	-0.1942	-0.0646	-0.0541	0.0422	0.0039	-0.0103	0.0119	0.0006	0.0214	-13.9543	5.1573	-42.6774
2	0.4968	0.2388	0.1118	0.6293	0.0401	0.8038	-0.0259	-0.0503	0.0991	-0.0314	-0.0209	0.0515	-0.1519	-0.0913	0.0468	0.0338	0.0211	-0.0107	0.0164	-0.0132	0.0207	-21.3931	5.1581	-36.5516
3	2.3002	-0.8235	-1.5342	0.8935	0.4104	3.2812	0.1178	0.0794	0.2404	-0.1061	-0.0489	-0.0211	-0.2989	-0.1035	-0.0689	0.0789	0.0253	-0.0084	0.0095	0.0014	0.0411	-24.0919	14.0542	-41.317
4	0.725	-0.156	-0.0164	0.7491	-0.0773	0.7466	-0.0453	-0.0046	-0.0405	-0.0716	0.0357	0.0903	-0.0061	-0.1308	0.0096	0.0141	0.0032	-0.0084	0.0451	-0.0054	0.014	-27.6378	-8.8211	-46.615
5	0.5954	0.1785	0.0087	0.3258	0.0924	0.7041	-0.0116	0.0231	-0.0571	-0.0273	-0.0154	0.0056	0.0741	0.0279	0.027	0.0257	0.0053	0.0004	0.0194	-0.0045	0.0082	-12.9843	-12.9056	-46.7315
6	0.807	0.0149	-0.051	0.6091	0.4191	0.973	-0.0034	0.015	-0.0235	0.0212	-0.0064	-0.0681	0.0543	0.1285	0.0097	0.0177	0.0042	0.0003	0.0435	0.0121	0.0127	-1.4899	-8.6737	-46.2423
7	0.7543	-0.5117	-0.2808	1.2211	0.7724	1.7095	0.0562	0.0263	0.0736	-0.0799	-0.0378	-0.0719	-0.149	0.134	-0.0184	0.0159	-0.0138	0.004	0.0317	0.0076	0.0084	-4.2487	-1.8315	-46.4743
8	3.5356	-0.5542	-3.0754	2.2407	1.194	4.4307	0.0295	-0.1627	0.1312	0.0206	-0.0334	-0.1568	-0.1844	0.3014	0.0039	0.0237	-0.0247	-0.0129	0.0376	0.0153	0.0418	-1.8834	8.1748	-40.3601
9	2.2399	-0.6367	1.3141	2.0118	-1.0215	2.1434	0.0326	-0.2071	-0.2075	0.1072	0.0011	0.0594	0.1316	-0.1066	-0.0337	0.0366	0.0013	0.0005	0.0307	0.0095	0.0348	-20.009	-24.9982	-11.4588
10	0.4167	0.0642	-0.1417	0.7763	0.1186	0.5266	-0.0009	0.0283	-0.0393	-0.0402	-0.027	0.0967	0.0061	-0.0856	0.0278	0.009	0.0066	-0.0102	0.022	-0.0115	0.0211	-29.1686	-14.9263	-20.9176
11	3.0087	-1.2224	0.6371	0.5994	-0.5324	1.6363	0.0333	-0.1309	-0.2952	-0.0163	0.0453	0.1602	0.1218	-0.1081	-0.0786	0.0194	-0.0085	-0.0005	0.0321	-0.013	0.0868	-35.8506	-18.7887	-13.3908
12	0.3792	-0.0963	0.0241	0.6375	0.1089	0.64	0.0177	0.0082	0.0243	0.0356	-0.0141	-0.0132	-0.0627	0.0011	-0.0036	0.0179	0.0059	-0.0054	0.0076	-0.0064	0.0085	-18.4412	-2.7467	-10.9824
13	0.6584	-0.0332	0.005	0.6601	0.2694	0.3064	-0.0016	0.0046	0.0155	-0.0057	0.0154	-0.0603	0.0154	0.0706	-0.0138	0.0112	0.0121	-0.006	0.0258	-0.0029	0.0121	-4.674	-13.9218	-15.5734
14	0.8114	0.011	0.2289	0.741	0.1622	0.5486	-0.005	0.0505	-0.081	0.0052	0.0123	-0.04	0.0949	0.0428	-0.0073	0.0332	0.0153	-0.0041	0.0153	-0.0087	0.021	-8.0063	-27.3248	-20.045
15	3.3071	0.1623	-0.641	1.0852	0.0174	1.2001	-0.0666	-0.2264	-0.1568	0.1359	0.0386	-0.0732	0.1267	0.0953	0.0279	0.0629	0.0289	-0.0284	0.0259	0.0004	0.033	-2.9515	-28.2904	-9.9621
16	1.7333	-0.5075	0.78	2.7024	-0.6601	1.5224	0.0082	0.0392	-0.1764	-0.1104	-0.0084	0.0333	0.1835	-0.0013	0.0002	0.0356	0.0043	0.0072	0.0082	-0.0093	0.0257	-20.4719	-28.7228	-22.4984

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	30 - 44
2	X-RAY DIFFRACTION	2	A	45 - 79
3	X-RAY DIFFRACTION	3	A	80 - 101
4	X-RAY DIFFRACTION	4	A	102 - 181
5	X-RAY DIFFRACTION	5	A	182 - 239
6	X-RAY DIFFRACTION	6	A	240 - 316
7	X-RAY DIFFRACTION	7	A	317 - 339
8	X-RAY DIFFRACTION	8	A	340 - 356
9	X-RAY DIFFRACTION	9	B	30 - 39
10	X-RAY DIFFRACTION	10	B	40 - 79
11	X-RAY DIFFRACTION	11	B	80 - 102
12	X-RAY DIFFRACTION	12	B	103 - 181
13	X-RAY DIFFRACTION	13	B	182 - 270
14	X-RAY DIFFRACTION	14	B	271 - 316
15	X-RAY DIFFRACTION	15	B	317 - 329
16	X-RAY DIFFRACTION	16	B	330 - 356

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