PDB-3ox6: Crystal Structure of the calcium sensor calcium-binding protein 1...

ID or keywords:

Entry

Database: PDB / ID: 3ox6

Title

Crystal Structure of the calcium sensor calcium-binding protein 1 (CaBP1)

Components

Calcium-binding protein 1

Keywords

calcium binding protein / EF-hand / Calcium-sensor / calcium binding

Function / homology

Function and homology information

nuclear localization sequence binding / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of protein import into nucleus / enzyme inhibitor activity / visual perception / calcium channel regulator activity / calcium-dependent protein binding / cell cortex / cytoskeleton / postsynaptic density ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Findeisen, F. / Minor, D.L.

Citation

Journal: Structure / Year: 2010
Title: Structural Basis for the Differential Effects of CaBP1 and Calmodulin on Ca(V)1.2 Calcium-Dependent Inactivation.
Authors: Findeisen, F. / Minor, D.L.

History

Deposition	Sep 21, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ox6.cif.gz	369.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3ox6.ent.gz	305 KB	Display	PDB format
PDBx/mmJSON format	3ox6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ox6_validation.pdf.gz	491.8 KB	Display	wwPDB validaton report
Full document	3ox6_full_validation.pdf.gz	520.9 KB	Display
Data in XML	3ox6_validation.xml.gz	35.2 KB	Display
Data in CIF	3ox6_validation.cif.gz	47.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ox/3ox6 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/3ox6	HTTPS FTP

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Related structure data

Related structure data	3ox5C C: citing same article (ref.)
Similar structure data	3ox5-5 3ox5-1 3ox5-4 3ox5-3 3ox5-2 6nxk-2 3ox5-6 3mhx-d 6nxk-1 1gmu-3 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) 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

3ox5C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Calcium-binding protein 1

B: Calcium-binding protein 1

C: Calcium-binding protein 1

D: Calcium-binding protein 1

E: Calcium-binding protein 1

F: Calcium-binding protein 1

hetero molecules

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

1

A: Calcium-binding protein 1

hetero molecules

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

2

B: Calcium-binding protein 1

hetero molecules

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

3

C: Calcium-binding protein 1

hetero molecules

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

4

D: Calcium-binding protein 1

hetero molecules

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

5

E: Calcium-binding protein 1

hetero molecules

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

6

F: Calcium-binding protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.716, 68.716, 344.195
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

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
1	2	B
2	2	A
3	2	D
4	2	C
1	3	B
2	3	A
3	3	C
4	3	F
5	3	E

NCS ensembles :

ID
1
2
3

#1: Protein	Calcium-binding protein 1 / CaBP1 / Caldendrin / Calbrain Mass: 17764.975 Da / Num. of mol.: 6 / Fragment: UNP residues 219-370 / Mutation: K130A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CABP1 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q9NZU7
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-HEZ / HEXANE-1,6-DIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.2 Å³/Da / Density % sol: 44.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.9M (NH4)2SO4, 5-7% 1,6-hexanediol, 0.1M citrate/sodium citrate pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 0.97958, 0.97972, 1.01987

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2008

Radiation

Monochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97958	1
2	0.97972	1
3	1.01987	1

Reflection

Resolution: 2.4→50 Å / Num. all: 38309 / Num. obs: 38103 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / R_sym value: 0.072 / Net I/σ(I): 7.1

Reflection shell

Resolution: 2.4→2.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.6 / R_sym value: 0.432 / % possible all: 99

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHELXS		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.4→15 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.901 / SU B: 27.78 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.579 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29528	1944	5.1 %	RANDOM
R_work	0.25218	-	-	-
obs	0.25436	35928	99.4 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 90.926 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.11 Å²	-0.06 Å²	0 Å²
2-	-	-0.11 Å²	0 Å²
3-	-	-	0.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6800	0	43	108	6951

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	6947
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.556	1.975	9313
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.686	5	875
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.995	24.712	382
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.497	15	1266
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.208	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1003
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5364
X-RAY DIFFRACTION	r_gen_planes_other
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	1.854	3	4317
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.001	4	6863
X-RAY DIFFRACTION	r_scbond_it	2.383	3	2630
X-RAY DIFFRACTION	r_scangle_it	3.545	4	2443
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	262	tight positional	0.16	0.01
1	1	B	262	tight positional	0.17	0.01
1	1	C	262	tight positional	0.13	0.01
1	1	D	262	tight positional	0.14	0.01
1	1	E	262	tight positional	0.14	0.01
1	1	F	262	tight positional	0.17	0.01
2	2	A	32	tight positional	0.06	0.01
2	2	B	32	tight positional	0.08	0.01
2	2	C	32	tight positional	0.07	0.01
2	2	D	32	tight positional	0.07	0.01
1	1	A	241	medium positional	0.33	0.1
1	1	B	241	medium positional	0.33	0.1
1	1	C	241	medium positional	0.32	0.1
1	1	D	241	medium positional	0.27	0.1
1	1	E	241	medium positional	0.26	0.1
1	1	F	241	medium positional	0.3	0.1
2	2	A	123	medium positional	0.16	0.1
2	2	B	123	medium positional	0.2	0.1
2	2	C	123	medium positional	0.26	0.1
2	2	D	123	medium positional	0.18	0.1
3	3	A	75	medium positional	0.13	0.1
3	3	B	75	medium positional	0.13	0.1
3	3	C	75	medium positional	0.11	0.1
3	3	D	75	medium positional	0.1	0.1
3	3	E	75	medium positional	0.12	0.1
2	2	A	78	loose positional	0.27	1
2	2	B	78	loose positional	0.33	1
2	2	C	78	loose positional	0.28	1
2	2	D	78	loose positional	0.4	1
3	3	A	80	loose positional	0.29	1
3	3	B	80	loose positional	0.24	1
3	3	C	80	loose positional	0.35	1
3	3	D	80	loose positional	0.21	1
3	3	E	80	loose positional	0.31	1
1	1	A	262	tight thermal	4.29	40
1	1	B	262	tight thermal	4.72	40
1	1	C	262	tight thermal	16.54	40
1	1	D	262	tight thermal	8.47	40
1	1	E	262	tight thermal	9.88	40
1	1	F	262	tight thermal	21.34	40
2	2	A	32	tight thermal	6.98	40
2	2	B	32	tight thermal	6.93	40
2	2	C	32	tight thermal	5.92	40
2	2	D	32	tight thermal	5.04	40
1	1	A	241	medium thermal	5.14
1	1	B	241	medium thermal	5.53
1	1	C	241	medium thermal	16.19
1	1	D	241	medium thermal	8.32
1	1	E	241	medium thermal	9.38
1	1	F	241	medium thermal	21.38
2	2	A	123	medium thermal	5.01
2	2	B	123	medium thermal	6.38
2	2	C	123	medium thermal	10.43
2	2	D	123	medium thermal	7.8
3	3	A	75	medium thermal	5.21
3	3	B	75	medium thermal	6.49
3	3	C	75	medium thermal	5.32
3	3	D	75	medium thermal	15.72
3	3	E	75	medium thermal	20
2	2	A	78	loose thermal	4.93
2	2	B	78	loose thermal	7.59
2	2	C	78	loose thermal	11.57
2	2	D	78	loose thermal	7.93
3	3	A	80	loose thermal	7.36
3	3	B	80	loose thermal	6.72
3	3	C	80	loose thermal	5.12
3	3	D	80	loose thermal	15.12
3	3	E	80	loose thermal	20.64

LS refinement shell

Resolution: 2.4→2.461 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.338	144	-
R_work	0.286	2543	-
obs	-	-	98.39 %

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	7.4888	-0.7884	0.1287	7.65	2.8903	5.7193	0.0746	0.2205	-1.0403	0.1115	-0.5696	1.4224	0.2211	-0.4096	0.495	0.0591	-0.0089	0.0611	0.3525	-0.0229	0.4943	-4.506	-5.494	17.546
2	6.3501	-2.5909	0.368	6.6315	-4.6572	7.5127	-0.4226	-0.5562	0.9197	1.4341	0.0696	-0.213	-1.2503	0.0087	0.353	0.4466	0.0272	-0.0489	0.2217	-0.135	0.2071	4.993	20.152	17.351
3	1.8763	-0.8348	-0.15	6.4721	-0.757	3.9829	0.0909	0.47	0.4608	-0.5904	0.3233	-0.5176	-0.4843	-0.0837	-0.4142	0.1443	-0.0292	0.1087	0.2358	0.0451	0.2122	23.776	10.103	4.779
4	4.4443	-3.0346	-0.4984	8.4724	1.5064	3.9612	0.0169	0.2152	-0.9236	0.1741	0.0389	0.5023	0.7655	-0.0988	-0.0558	0.1558	0.0007	-0.0352	0.1062	-0.0465	0.1998	16.91	-15.442	11.651
5	5.3257	-0.9099	-1.5252	6.4213	1.7929	5.0078	-0.1735	-0.122	-0.1968	-0.115	0.5145	-1.1597	0.2014	0.9094	-0.341	0.2356	0.0568	-0.1032	0.4083	-0.179	0.5249	37.628	-5.637	14.919
6	6.2311	0.7886	2.8134	5.75	0.8691	8.1829	-0.0794	-0.03	1.1523	0.5554	0.2235	-0.5219	-1.3377	0.5198	-0.1441	0.6486	-0.0394	-0.1184	0.3597	-0.1958	0.7017	33.26	20.022	23.925
7	5.4999	-1.0929	-1.9353	3.0955	1.0681	9.8361	0.2277	-0.9143	0.0915	-0.2815	0.2023	-0.1822	-2.1282	0.9539	-0.4301	0.7454	-0.0872	-0.0342	0.5474	-0.1627	0.1053	35.318	9.923	45.622
8	8.82	-0.9328	-2.1486	3.9247	-1.7827	13.1664	-0.6929	-0.6962	-1.4051	-0.0711	0.094	0.0009	1.8538	0.1476	0.5989	0.5472	0.1579	-0.008	0.466	0.0251	0.318	31.901	-15.326	35.945
9	3.9967	-0.3138	1.5175	5.9213	-1.9704	6.2559	-0.0257	-1.0253	0.2018	0.7462	0.4783	-0.0566	0.0294	-0.9243	-0.4526	0.814	0.1491	0.035	1.4441	0.055	0.4755	19.932	-4.538	52.849
10	7.6926	6.8837	4.5612	9.4389	5.5056	11.2634	-1.1498	-0.7738	0.9179	-1.4381	0.0547	0.3125	-2.9021	-0.8243	1.0951	2.0702	0.4153	-0.2417	1.1633	-0.372	0.3333	18.519	22.053	41.594
11	5.5092	-0.584	-2.9642	9.8624	-1.9213	11.617	0.1295	-1.6779	0.3378	1.8155	0.0292	1.4924	-1.7467	-0.2304	-0.1586	0.6956	0.0042	0.3109	1.1497	-0.15	0.3036	-7.234	9.126	34.521
12	13.7982	2.1128	5.3158	5.3944	2.0563	5.4249	1.2835	-2.4895	-2.0332	1.5263	-0.8618	0.5545	1.7542	-0.2309	-0.4217	1.0186	-0.2931	0.0964	1.0801	0.4493	0.5259	2.99	-15.058	37.333

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 99
2	X-RAY DIFFRACTION	2	A	100 - 167
3	X-RAY DIFFRACTION	2	A	501 - 502
4	X-RAY DIFFRACTION	2	A	603 - 604
5	X-RAY DIFFRACTION	3	B	15 - 99
6	X-RAY DIFFRACTION	4	B	100 - 167
7	X-RAY DIFFRACTION	4	B	501 - 502
8	X-RAY DIFFRACTION	4	B	601 - 602
9	X-RAY DIFFRACTION	5	C	15 - 99
10	X-RAY DIFFRACTION	6	C	100 - 167
11	X-RAY DIFFRACTION	6	C	501 - 502
12	X-RAY DIFFRACTION	7	D	15 - 99
13	X-RAY DIFFRACTION	8	D	100 - 167
14	X-RAY DIFFRACTION	8	D	501 - 502
15	X-RAY DIFFRACTION	9	E	15 - 99
16	X-RAY DIFFRACTION	10	E	133 - 167
17	X-RAY DIFFRACTION	10	E	502
18	X-RAY DIFFRACTION	11	F	15 - 99
19	X-RAY DIFFRACTION	12	F	100 - 167
20	X-RAY DIFFRACTION	12	F	501 - 502

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About Yorodumi

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Yorodumi