PDB-2w01: Crystal structure of the guanylyl cyclase Cya2

ID or keywords:

Entry

Database: PDB / ID: 2w01

Title

Crystal structure of the guanylyl cyclase Cya2

Components

ADENYLATE CYCLASE

Keywords

LYASE / GUANYLYL CYCLASE / CLASS III NUCLEOTIDYL CYCLASE

Function / homology

Function and homology information

cyclic nucleotide biosynthetic process / adenylate cyclase activity / intracellular signal transduction / identical protein binding
Similarity search - Function

Biological species

SYNECHOCYSTIS SP. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.31 Å

Authors

Rauch, A. / Leipelt, M. / Russwurm, M. / Steegborn, C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal Structure of the Guanylyl Cyclase Cya2.
Authors: Rauch, A. / Leipelt, M. / Russwurm, M. / Steegborn, C.

History

Deposition	Aug 8, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 30, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2w01.cif.gz	238.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2w01.ent.gz	193.1 KB	Display	PDB format
PDBx/mmJSON format	2w01.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/w0/2w01 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w01	HTTPS FTP

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Related structure data

Related structure data	1wc1S S: Starting model for refinement
Similar structure data	3a04-d 4arv-2 3rj8-d 4arv-1 4lev-1 3e34-3 3noq-d 6ni8-d 6b4h-1 7ld6-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1wc1S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#251 - Nov 2020 Adenylyl Cyclase similarity (5) #133 - Jan 2011 Nitric Oxide Synthase similarity (5) #58 - Oct 2004 G Proteins similarity (5)

Deposited unit

A: ADENYLATE CYCLASE

B: ADENYLATE CYCLASE

C: ADENYLATE CYCLASE

D: ADENYLATE CYCLASE

E: ADENYLATE CYCLASE

F: ADENYLATE CYCLASE

133 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ADENYLATE CYCLASE

B: ADENYLATE CYCLASE

defined by author&software
44.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ADENYLATE CYCLASE

D: ADENYLATE CYCLASE

defined by author&software
44.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: ADENYLATE CYCLASE

F: ADENYLATE CYCLASE

defined by author&software
44.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.445, 84.090, 115.328
Angle α, β, γ (deg.)	90.00, 97.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
3	1	D
4	1	C
5	1	F
6	1	E

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	ARG	ARG	5	B	B	438 - 450	11 - 23
2	1	ASP	ASP	ARG	ARG	5	A	A	438 - 450	11 - 23
3	1	ASP	ASP	ARG	ARG	5	D	D	438 - 450	11 - 23
4	1	ASP	ASP	ARG	ARG	5	C	C	438 - 450	11 - 23
5	1	ASP	ASP	ARG	ARG	5	F	F	438 - 450	11 - 23
6	1	ASP	ASP	ARG	ARG	5	E	E	438 - 450	11 - 23
1	2	PHE	PHE	GLU	GLU	6	B	B	452 - 457	25 - 30
2	2	PHE	PHE	GLU	GLU	6	A	A	452 - 457	25 - 30
3	2	PHE	PHE	GLU	GLU	6	D	D	452 - 457	25 - 30
4	2	PHE	PHE	GLU	GLU	6	C	C	452 - 457	25 - 30
5	2	PHE	PHE	GLU	GLU	6	F	F	452 - 457	25 - 30
6	2	PHE	PHE	GLU	GLU	6	E	E	452 - 457	25 - 30
1	3	VAL	VAL	PHE	PHE	5	B	B	465 - 489	38 - 62
2	3	VAL	VAL	PHE	PHE	5	A	A	465 - 489	38 - 62
3	3	VAL	VAL	PHE	PHE	5	D	D	465 - 489	38 - 62
4	3	VAL	VAL	PHE	PHE	5	C	C	465 - 489	38 - 62
5	3	VAL	VAL	PHE	PHE	5	F	F	465 - 489	38 - 62
6	3	VAL	VAL	PHE	PHE	5	E	E	465 - 489	38 - 62
1	4	GLY	GLY	PHE	PHE	5	B	B	493 - 498	66 - 71
2	4	GLY	GLY	PHE	PHE	5	A	A	493 - 498	66 - 71
3	4	GLY	GLY	PHE	PHE	5	D	D	493 - 498	66 - 71
4	4	GLY	GLY	PHE	PHE	5	C	C	493 - 498	66 - 71
5	4	GLY	GLY	PHE	PHE	5	F	F	493 - 498	66 - 71
6	4	GLY	GLY	PHE	PHE	5	E	E	493 - 498	66 - 71
1	5	GLY	GLY	SER	SER	6	B	B	499 - 503	72 - 76
2	5	GLY	GLY	SER	SER	6	A	A	499 - 503	72 - 76
3	5	GLY	GLY	SER	SER	6	D	D	499 - 503	72 - 76
4	5	GLY	GLY	SER	SER	6	C	C	499 - 503	72 - 76
5	5	GLY	GLY	SER	SER	6	F	F	499 - 503	72 - 76
6	5	GLY	GLY	SER	SER	6	E	E	499 - 503	72 - 76
1	6	LEU	LEU	VAL	VAL	6	B	B	509 - 525	82 - 98
2	6	LEU	LEU	VAL	VAL	6	A	A	509 - 525	82 - 98
3	6	LEU	LEU	VAL	VAL	6	D	D	509 - 525	82 - 98
4	6	LEU	LEU	VAL	VAL	6	C	C	509 - 525	82 - 98
5	6	LEU	LEU	VAL	VAL	6	F	F	509 - 525	82 - 98
6	6	LEU	LEU	VAL	VAL	6	E	E	509 - 525	82 - 98
1	7	LEU	LEU	VAL	VAL	6	B	B	537 - 550	110 - 123
2	7	LEU	LEU	VAL	VAL	6	A	A	537 - 550	110 - 123
3	7	LEU	LEU	VAL	VAL	6	D	D	537 - 550	110 - 123
4	7	LEU	LEU	VAL	VAL	6	C	C	537 - 550	110 - 123
5	7	LEU	LEU	VAL	VAL	6	F	F	537 - 550	110 - 123
6	7	LEU	LEU	VAL	VAL	6	E	E	537 - 550	110 - 123
1	8	VAL	VAL	THR	THR	5	B	B	563 - 588	136 - 161
2	8	VAL	VAL	THR	THR	5	A	A	563 - 588	136 - 161
3	8	VAL	VAL	THR	THR	5	D	D	563 - 588	136 - 161
4	8	VAL	VAL	THR	THR	5	C	C	563 - 588	136 - 161
5	8	VAL	VAL	THR	THR	5	F	F	563 - 588	136 - 161
6	8	VAL	VAL	THR	THR	5	E	E	563 - 588	136 - 161
1	9	THR	THR	HIS	HIS	6	B	B	589 - 598	162 - 171
2	9	THR	THR	HIS	HIS	6	A	A	589 - 598	162 - 171
3	9	THR	THR	HIS	HIS	6	D	D	589 - 598	162 - 171
4	9	THR	THR	HIS	HIS	6	C	C	589 - 598	162 - 171
5	9	THR	THR	HIS	HIS	6	F	F	589 - 598	162 - 171
6	9	THR	THR	HIS	HIS	6	E	E	589 - 598	162 - 171
1	10	ASP	ASP	SER	SER	6	B	B	618 - 629	191 - 202
2	10	ASP	ASP	SER	SER	6	A	A	618 - 629	191 - 202
3	10	ASP	ASP	SER	SER	6	D	D	618 - 629	191 - 202
4	10	ASP	ASP	SER	SER	6	C	C	618 - 629	191 - 202
5	10	ASP	ASP	SER	SER	6	F	F	618 - 629	191 - 202
6	10	ASP	ASP	SER	SER	6	E	E	618 - 629	191 - 202

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.8912, -0.2597, 0.3718), (-0.2561, -0.3884, -0.885), (0.3743, -0.8841, 0.2797)	9.313, -65.27, -47.56
2	given	(0.9043, -0.06519, 0.4218), (0.2494, 0.8827, -0.3982), (-0.3464, 0.4653, 0.8145)	46.4, -13.55, 32
3	given	(-0.9998, 0.000978, -0.02079), (0.01352, -0.7289, -0.6845), (-0.01582, -0.6847, 0.7287)	-21.4, -100.2, -11.35
4	given	(0.9996, -0.02795, -0.001531), (-0.02132, -0.7249, -0.6885), (0.01813, 0.6883, -0.7252)	-23.63, -72.43, -129.6
5	given	(-0.9005, 0.4232, -0.09958), (-0.2489, -0.3141, 0.9162), (0.3565, 0.8498, 0.3882)	0.5378, 84.24, -30.05

#1: Protein	ADENYLATE CYCLASE / GUANYLYL CYCLASE CYA2 Mass: 22210.057 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 434-635 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P72951, guanylate cyclase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	6 N-TERMINAL RESIDUES ARE CLONING ARTIFACT

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 45.79 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 50776 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 3 % / R_merge(I) obs: 0.38 / % possible all: 85

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WC1

1wc1

Resolution: 2.31→19.94 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.894 / SU B: 17.65 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.282	2597	5.1 %	RANDOM
R_work	0.194	-	-	-
obs	0.198	48079	97 %	-

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: 41.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0.08 Å²
2-	-	0.17 Å²	0 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→19.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8911	0	0	468	9379

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	9037
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.922	1.964	12259
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.169	5	1187
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.796	24.974	382
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.863	15	1512
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.384	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	1443
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6780
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.253	0.2	4183
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	6054
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.204	0.2	435
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	0.292	0.2	142
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.243	0.2	16
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	0.943	1.5	6007
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.597	2	9416
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.431	3	3377
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.845	4.5	2843
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	B	280	medium positional	0.19	0.5
2	A	280	medium positional	0.18	0.5
3	D	280	medium positional	0.21	0.5
4	C	280	medium positional	0.17	0.5
5	F	280	medium positional	0.27	0.5
6	E	280	medium positional	0.18	0.5
1	B	727	loose positional	0.63	5
2	A	727	loose positional	0.65	5
3	D	727	loose positional	0.64	5
4	C	727	loose positional	0.63	5
5	F	727	loose positional	0.71	5
6	E	727	loose positional	0.72	5
1	B	280	medium thermal	1.48	2
2	A	280	medium thermal	1.62	2
3	D	280	medium thermal	0.91	2
4	C	280	medium thermal	1.83	2
5	F	280	medium thermal	1.61	2
6	E	280	medium thermal	1.22	2
1	B	727	loose thermal	3.2	10
2	A	727	loose thermal	4.49	10
3	D	727	loose thermal	3.04	10
4	C	727	loose thermal	3.92	10
5	F	727	loose thermal	4.42	10
6	E	727	loose thermal	2.97	10

LS refinement shell

Resolution: 2.31→2.37 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.36	164
R_work	0.232	2849

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	2.9275	-1.1565	-1.3275	1.4723	0.8444	1.1159	-0.0064	-0.3006	0.0584	0.0528	0.0459	0.0167	-0.0408	0.2285	-0.0394	-0.079	-0.0238	-0.0381	-0.0473	-0.0638	-0.0979	-16.418	-15.493	-54.842
2	2.1569	0.1596	0.2866	1.5696	0.6978	0.681	-0.0101	0.0527	0.0789	-0.0179	-0.0376	0.0817	0.0056	-0.0412	0.0477	-0.0821	-0.0298	-0.0097	-0.1061	-0.0193	-0.1146	8.113	-6.206	-55.103
3	3.3705	-0.6593	0.5835	1.7245	0.188	0.7677	0.0017	0.0529	0.1751	-0.1381	0.0929	-0.287	0.0216	-0.0412	-0.0946	-0.0483	-0.0033	0.0066	-0.1586	0.0192	-0.0413	-27.074	-38.197	-96.884
4	3.3571	-0.2092	0.3186	0.8599	-0.3778	1.6911	-0.0361	0.0989	0.2202	-0.0487	-0.0638	-0.033	0.0524	0.0628	0.1	-0.0485	0.0123	-0.0204	-0.184	-0.0098	-0.1059	-2.982	-31.828	-90.181
5	1.9254	-0.744	-0.9703	1.0097	-0.2006	3.4117	0.2714	-0.4935	0.5329	0.0294	-0.045	0.0503	-0.1424	0.3361	-0.2264	-0.0091	-0.0756	0.0485	0.1664	-0.1543	0.1518	7.156	9.997	-93.654
6	5.8202	0.541	2.0902	1.7484	0.6301	1.9509	0.0501	-0.6288	-0.1011	-0.1622	-0.1596	-0.1591	0.0489	-0.2249	0.1095	-0.0347	0.0485	0.0108	-0.0994	0.1056	-0.0803	31.224	2.382	-99.289

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	435 - 631
2	X-RAY DIFFRACTION	2	A	435 - 635
3	X-RAY DIFFRACTION	3	D	434 - 632
4	X-RAY DIFFRACTION	4	C	434 - 633
5	X-RAY DIFFRACTION	5	F	435 - 631
6	X-RAY DIFFRACTION	6	E	434 - 632

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