PDB-2fgy: Beta Carbonic Anhydrase from the Carboxysomal Shell of Halothioba...

ID or keywords:

Entry

Database: PDB / ID: 2fgy

Title

Beta Carbonic Anhydrase from the Carboxysomal Shell of Halothiobacillus neapolitanus (CsoSCA)

Components

carboxysome shell polypeptide

Keywords

LYASE / beta class of carbonic anhydrase

Function / homology

Function and homology information

carboxysome / carbonic anhydrase / carbonate dehydratase activity
Similarity search - Function

Biological species

Halothiobacillus neapolitanus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.2 Å

Authors

Sawaya, M.R.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: The Structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.
Authors: Sawaya, M.R. / Cannon, G.C. / Heinhorst, S. / Tanaka, S. / Williams, E.B. / Yeates, T.O. / Kerfeld, C.A.

History

Deposition	Dec 22, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 17, 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
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr2_auth_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 / _struct_conn.pdbx_dist_value / _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_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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Nov 13, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2fgy.cif.gz	209.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2fgy.ent.gz	163.3 KB	Display	PDB format
PDBx/mmJSON format	2fgy.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/fg/2fgy ftp://data.pdbj.org/pub/pdb/validation_reports/fg/2fgy	HTTPS FTP

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Related structure data

Similar structure data	6f73-d 7a0p-d 3k99-d 4c0d-d 5l8w-d 4psw-d 6yks-d 22990 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: carboxysome shell polypeptide

B: carboxysome shell polypeptide

hetero molecules

122 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)	47.738, 77.636, 82.714
Angle α, β, γ (deg.)	66.84, 78.82, 79.17
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B
3	1	A
4	1	B
1	2	A
2	2	B
1	3	A
2	3	B

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	HIS	GLY	GLY	A	A	38 - 89	66 - 117
2	1	1	HIS	HIS	GLY	GLY	B	B	38 - 89	66 - 117
3	2	1	ASP	ASP	ASN	ASN	A	A	91 - 116	119 - 144
4	2	1	ASP	ASP	ASN	ASN	B	B	91 - 116	119 - 144
1	1	2	ILE	ILE	ASN	ASN	A	A	118 - 348	146 - 376
2	1	2	ILE	ILE	ASN	ASN	B	B	118 - 348	146 - 376
1	1	3	SER	SER	ALA	ALA	A	A	350 - 514	378 - 542
2	1	3	SER	SER	ALA	ALA	B	B	350 - 514	378 - 542

NCS ensembles :

ID
1
2
3

Details

The biological assembly is a dimer. It is contained in the asymmetric unit.

#1: Protein	carboxysome shell polypeptide Mass: 60718.145 Da / Num. of mol.: 2 / Mutation: Y92H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria) Description: Gene name is previously known as CsoS3 / Gene: CsoSCA / Plasmid: pcsoS3ProEx / Production host: Escherichia coli (E. coli) References: GenBank: 3449369, UniProt: O85042*PLUS, carbonic anhydrase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H₂O
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: 2.39 Å³/Da / Density % sol: 48.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, pH 7.0, 0.2M magnesium chloride, 10% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2005 / Details: KOHZU: Double Crystal Si(111)
Radiation	Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.2→90 Å / Num. all: 52342 / Num. obs: 52789 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / B_iso Wilson estimate: 44.1 Å² / R_merge(I) obs: 0.123 / Χ²: 1.089
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.488 / Num. unique all: 5120 / Χ²: 1.215 / % possible all: 94.7

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Phasing

Phasing

Method:

MIRAS

Phasing MAD

D res high: 2.2 Å / D res low: 75.38 Å

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 52789

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.25-100	46.9	0.714	513
7.77-10.25	47.6	0.883	675
6.51-7.77	47.7	0.868	862
5.72-6.51	55	0.838	999
5.15-5.72	55.5	0.821	1085
4.73-5.15	54.7	0.847	1231
4.4-4.73	56.5	0.84	1312
4.13-4.4	59	0.808	1416
3.9-4.13	58.9	0.78	1511
3.71-3.9	66.3	0.762	1565
3.54-3.71	65.5	0.739	1655
3.39-3.54	64.8	0.753	1724
3.26-3.39	67.3	0.729	1816
3.15-3.26	70.8	0.704	1863
3.04-3.15	72.6	0.673	1938
2.95-3.04	73.3	0.693	1996
2.86-2.95	78.5	0.637	2032
2.78-2.86	88.4	0.594	2112
2.71-2.78	86.9	0.574	2201
2.64-2.71	88.7	0.587	2202
2.58-2.64	88.9	0.611	2245
2.52-2.58	90	0.599	2321
2.47-2.52	87.5	0.58	2414
2.42-2.47	88.5	0.532	2408
2.37-2.42	89.2	0.58	2484
2.32-2.37	90.7	0.565	2527
2.28-2.32	90.3	0.594	2547
2.24-2.28	90.6	0.575	2545
2.2-2.24	88	0.544	2590

Phasing MIR der

R cullis centric: 0 / Der set-ID: 1 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

ID	Resolution (Å)	R cullis acentric	Loc acentric	Power acentric	Reflection acentric
Mercury Chloride	3.3-100	0.81	36.4	1.13	15478
mersalyl	3-100	0.83	28.7	1.05	20545
PIP from isodifou using p	3.8-100	0.94	66.2	0.56	10176
native Zn from anodifou u	2.2-100	1	3.8	0	52337
iodide from isodifou usin	3.9-100	0.92	69.8	0.76	9374

Phasing MIR der shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	R cullis acentric	Loc acentric	Power acentric	Reflection acentric
14.61	75.38	Mercury Chloride	0.47	28.5	2.58	161
8.09	14.61	Mercury Chloride	0.6	27.2	2.47	867
5.59	8.09	Mercury Chloride	0.63	24.9	2.27	2173
4.28	5.59	Mercury Chloride	0.77	33.3	1.35	3982
3.46	4.28	Mercury Chloride	0.88	41.4	0.81	6296
2.91	3.46	Mercury Chloride	0.92	43.9	0.62	1999
2.5	2.91	Mercury Chloride	0	0	0	0
2.2	2.5	Mercury Chloride	0	0	0	0
14.61	75.38	mersalyl	0.52	31.5	2.15	160
8.09	14.61	mersalyl	0.62	26.9	2.23	872
5.59	8.09	mersalyl	0.65	21.1	2.34	2172
4.28	5.59	mersalyl	0.76	26.1	1.45	3974
3.46	4.28	mersalyl	0.86	30	0.89	6297
2.91	3.46	mersalyl	0.94	31.4	0.59	7070
2.5	2.91	mersalyl	0	0	0	0
2.2	2.5	mersalyl	0	0	0	0
14.61	75.38	PIP from isodifou using p	0.87	92.1	0.8	164
8.09	14.61	PIP from isodifou using p	0.86	75.1	0.86	866
5.59	8.09	PIP from isodifou using p	0.88	53.9	0.91	2169
4.28	5.59	PIP from isodifou using p	0.96	65.1	0.52	3968
3.46	4.28	PIP from isodifou using p	0.98	72.7	0.32	3009
2.91	3.46	PIP from isodifou using p	0	0	0	0
2.5	2.91	PIP from isodifou using p	0	0	0	0
2.2	2.5	PIP from isodifou using p	0	0	0	0
14.61	75.38	native Zn from anodifou u	1	7.4	0	148
8.09	14.61	native Zn from anodifou u	1	7.8	0	799
5.59	8.09	native Zn from anodifou u	1	4.5	0	2168
4.28	5.59	native Zn from anodifou u	1	5.2	0	3901
3.46	4.28	native Zn from anodifou u	1	4.3	0	6296
2.91	3.46	native Zn from anodifou u	1	3	0	9410
2.5	2.91	native Zn from anodifou u	1	3.3	0	12906
2.2	2.5	native Zn from anodifou u	1	3.9	0	16709
14.61	75.38	iodide from isodifou usin	0.97	80.9	0.81	156
8.09	14.61	iodide from isodifou usin	0.97	75.8	0.82	871
5.59	8.09	iodide from isodifou usin	0.91	59.8	0.95	2173
4.28	5.59	iodide from isodifou usin	0.9	69.7	0.74	3977
3.46	4.28	iodide from isodifou usin	0.93	76.5	0.63	2197
2.91	3.46	iodide from isodifou usin	0	0	0	0
2.5	2.91	iodide from isodifou usin	0	0	0	0
2.2	2.5	iodide from isodifou usin	0	0	0	0

Phasing MIR der site

ID	Der-ID	B_iso (Å)	Atom type symbol	Fract x	Fract y	Fract z	Occupancy
1	Mercury Chloride	30.806	Hg	0.991	0.017	1	0.666
2	Mercury Chloride	37.723	Hg	1.354	-0.445	1.467	0.624
3	Mercury Chloride	67.399	Hg	1.319	-0.205	0.789	0.471
4	Mercury Chloride	59.044	Hg	1.307	-0.699	1.285	0.493
5	mersalyl	41.162	Hg	-0.005	0.014	0	0.648
6	mersalyl	50.634	Hg	1.356	0.556	0.466	0.554
7	mersalyl	68.796	Hg	1.323	0.796	0.787	0.39
8	mersalyl	68.278	Hg	1.304	0.3	1.286	0.424
9	PIP from isodifou using p	81.799	Pt	1.752	0.377	0.349	0.541
10	PIP from isodifou using p	65.227	Pt	1.16	0.236	0.372	0.652
11	PIP from isodifou using p	81.364	Pt	0.775	-0.133	0.85	0.621
12	PIP from isodifou using p	74.223	Pt	1.449	-0.123	0.726	0.588
13	native Zn from anodifou u	97.373	Zn	1.326	0.308	0.274	0
14	native Zn from anodifou u	114.13	Zn	0.796	-0.29	0.503	0
15	native Zn from anodifou u	100.96	Zn	2.067	-0.011	0.229	0
16	native Zn from anodifou u	105.77	Zn	1.299	-0.213	0.795	0
17	iodide from isodifou usin	60.7	I	1.344	0.247	0.721	0.425
18	iodide from isodifou usin	47.138	I	1.041	0.27	0.702	0.55
19	iodide from isodifou usin	44.284	I	1.319	-0.198	0.765	0.483
20	iodide from isodifou usin	27.562	I	1.326	0.274	0.29	0.66
21	iodide from isodifou usin	49.048	I	1.37	0.547	0.461	0.411
22	iodide from isodifou usin	-7.84	I	1.008	0.013	0.993	0.817

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction
BOS		data collection

Refinement

Method to determine structure:

MIRAS / Resolution: 2.2→75.38 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.926 / SU B: 9.909 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	2656	5 %	RANDOM
R_work	0.169	-	-	-
all	0.171	52788	-	-
obs	0.171	52788	97.84 %	-

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: 35.114 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.09 Å²	0.8 Å²	0.13 Å²
2-	-	-0.4 Å²	0.8 Å²
3-	-	-	-0.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→75.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7370	0	4	557	7931

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	7530
X-RAY DIFFRACTION	r_angle_refined_deg	1.617	1.951	10232
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.186	5	938
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.166	23.529	374
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.473	15	1212
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.326	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	1140
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5840
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	3452
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	5220
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	512
X-RAY DIFFRACTION	r_metal_ion_refined	0.033	0.2	2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.307	0.2	86
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.181	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.924	1.5	4817
X-RAY DIFFRACTION	r_mcangle_it	1.475	2	7542
X-RAY DIFFRACTION	r_scbond_it	2.482	3	3034
X-RAY DIFFRACTION	r_scangle_it	3.918	4.5	2690

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	612	TIGHT POSITIONAL	0.05	0.05
1	612	TIGHT THERMAL	0.17	0.5
2	1735	TIGHT POSITIONAL	0.05	0.05
2	1735	TIGHT THERMAL	0.18	0.5
3	1306	TIGHT POSITIONAL	0.04	0.05
3	1306	TIGHT THERMAL	0.18	0.5

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.307	186	-
R_work	0.217	3526	-
obs	-	3712	93.17 %

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	0.5565	0.2109	1.1735	1.5354	1.4047	3.1076	0.0484	-0.1511	-0.1616	0.0165	-0.1692	0.2784	0.1932	-0.3987	0.1208	-0.0825	-0.0715	0.0431	-0.0143	0.0048	0.0098	12.6086	27.8848	48.0212
2	0.3168	0.4259	-0.3882	0.8448	-0.3956	1.5187	-0.007	-0.091	-0.0488	0.107	-0.0041	-0.0739	0.0083	0.1378	0.011	-0.0359	0.0462	-0.0168	-0.0272	0.0098	-0.0648	35.8114	45.54	62.0024
3	0.91	0.1312	-0.1002	0.9274	-0.2816	1.0995	-0.0116	0.0497	0.0012	-0.0417	0.0055	0.0374	0.0634	-0.022	0.0062	-0.0559	0.0066	-0.0006	-0.0525	-0.0135	-0.0266	25.8713	38.4194	39.258
4	1.0688	-1.5992	0.1681	3.1245	0.2022	0.7403	0.0606	0.2861	0.0846	-0.1253	0.0641	-0.2031	0.0441	0.1106	-0.1247	-0.0827	-0.0071	0.0721	0.0432	-0.0204	-0.0432	62.87	50.9087	11.1532
5	0.6923	-0.2627	-0.3812	0.7962	-0.375	1.0687	0.0352	0.1585	0.1139	-0.0344	-0.007	-0.0186	-0.0754	-0.0488	-0.0282	-0.0314	0.0055	-0.0129	-0.0292	0.0435	-0.0306	39.542	71.2066	20.722
6	1.1264	-0.0219	-0.0944	0.6602	-0.3167	0.8491	-0.0183	0.0501	-0.0914	-0.023	0.0039	-0.0184	0.0739	0.0314	0.0144	-0.0534	0.0045	0.0055	-0.011	-0.0226	-0.0379	49.4912	47.6401	24.4244

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	38 - 144	66 - 172
2	2	A	A	151 - 397	179 - 425
3	3	A	A	398 - 514	426 - 542
4	4	B	B	38 - 144	66 - 172
5	5	B	B	151 - 397	179 - 425
6	6	B	B	398 - 514	426 - 542

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