PDB-3nsi: Crystal Structure of the Post-Refolded S100A3 Protein Expressed i...

ID or keywords:

Entry

Database: PDB / ID: 3nsi

Title

Crystal Structure of the Post-Refolded S100A3 Protein Expressed in Insect Cell

Components

Protein S100-A3

Keywords

METAL BINDING PROTEIN / EF-hand / Ca2+ / Zn2+-binding / Acethylation

Function / homology

Function and homology information

transition metal ion binding / calcium-dependent protein binding / calcium ion binding / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Unno, M. / Takahara, H. / Kizawa, K.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Refined crystal structures of human Ca(2+)/Zn(2+)-binding S100A3 protein characterized by two disulfide bridges
Authors: Unno, M. / Kawasaki, T. / Takahara, H. / Heizmann, C.W. / Kizawa, K.

History

Deposition	Jul 1, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jun 27, 2012	Group: Database references
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nsi.cif.gz	88.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3nsi.ent.gz	69.3 KB	Display	PDB format
PDBx/mmJSON format	3nsi.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/ns/3nsi ftp://data.pdbj.org/pub/pdb/validation_reports/ns/3nsi	HTTPS FTP

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Related structure data

Related structure data	3nskSC 3nslC 3nsoC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3nsk-d 4e2t-1 3ext-d 2zz7-d 1dl3-1 5dcx-6 3nso-d 5g4e-2 4e2t-2 3kts-6 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: Protein S100-A3

B: Protein S100-A3

23.5 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)	58.680, 58.680, 45.763
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-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	PRO	PRO	LEU	LEU	A	A	4 - 62	4 - 62
2	1	PRO	PRO	LEU	LEU	B	B	4 - 62	4 - 62
1	2	LYS	LYS	CYS	CYS	A	A	66 - 93	66 - 93
2	2	LYS	LYS	CYS	CYS	B	B	66 - 93	66 - 93

NCS ensembles :

ID
1
2

#1: Protein	Protein S100-A3 / S100 calcium-binding protein A3 / Protein S-100E Mass: 11725.416 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100A3, S100E / Cell line (production host): IPLB-Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33764
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.94 Å³/Da / Density % sol: 36.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Ammonium Sulfate, 0.1M Bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2009
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. all: 9695 / Num. obs: 9598 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.15→2.19 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
CNS		refinement
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-2000		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSK

3nsk

Resolution: 2.15→30 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.933 / SU B: 12.87 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23645	471	4.9 %	RANDOM
R_work	0.20341	-	-	-
all	0.20501	9695	-	-
obs	0.20501	9113	99.9 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 44.159 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.37 Å²	-0.19 Å²	0 Å²
2-	-	-0.37 Å²	0 Å²
3-	-	-	0.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1519	0	0	25	1544

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.022	1586
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.607	1.972	2165
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.486	5	203
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.839	24.789	71
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.23	15	263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.317	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.039	0.2	241
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.021	1205
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	1.522	1.5	987
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.744	2	1593
X-RAY DIFFRACTION	r_scbond_it	4.426	3	599
X-RAY DIFFRACTION	r_scangle_it	7.297	4.5	566
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	460	TIGHT POSITIONAL	0.05	0.05
1	460	TIGHT THERMAL	0.27	0.5
2	228	TIGHT POSITIONAL	0.12	0.05
2	228	TIGHT THERMAL	0.36	0.5

LS refinement shell

Resolution: 2.151→2.207 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.267	34	-
R_work	0.258	687	-
obs	-	-	100 %

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	4.3846	4.4467	3.6493	4.9182	3.3538	3.6158	-0.091	-0.059	0.143	-0.0818	0.1077	0.1403	-0.042	-0.1383	-0.0168	0.0267	0.0169	-0.0163	0.0792	-0.0177	0.1471	9.592	2.807	14.039
2	6.3739	1.851	3.6721	0.9598	1.3767	2.9285	0.0318	-0.0248	0.3678	-0.1055	-0.007	0.1136	-0.0949	-0.0278	-0.0248	0.0568	0.0052	-0.0044	0.0278	-0.0093	0.1902	21.788	10.038	11.73
3	5.6211	1.262	-1.6327	1.1283	-2.557	6.1563	-0.208	-0.1091	-0.1838	-0.1358	-0.011	-0.1038	0.3045	-0.0061	0.219	0.1386	-0.0105	-0.0527	0.0124	-0.0092	0.0885	5.947	-10.069	10.352
4	5.0831	2.8171	-4.6143	4.6139	0.0563	6.4272	-0.1001	-0.1958	-0.2781	-0.134	-0.1131	-0.21	0.0276	0.1728	0.2132	0.0334	0.0423	-0.0457	0.1032	-0.0488	0.1129	34.969	6.771	15.744
5	2.7084	0.6333	1.3471	10.0496	0.2284	0.6726	-0.1078	0.1263	-0.0043	-0.2329	0.1218	0.0181	-0.0377	0.058	-0.0141	0.0808	-0.0383	-0.0352	0.0494	-0.0051	0.0311	10.033	-1.554	1.516
6	10.0597	-2.8093	-1.4512	3.7737	1.2795	0.4728	0.0174	-0.3447	0.0767	0.0474	-0.0166	0.0537	0.0083	0.0452	-0.0008	0.0352	-0.0172	-0.0205	0.11	-0.0296	0.0295	25.669	7.482	24.499
7	10.0449	-2.1053	0.2015	4.9431	-0.0866	2.56	-0.0136	0.3507	0.2472	-0.4749	0.2468	-0.0915	0.1368	0.0288	-0.2332	0.0758	-0.041	-0.0052	0.039	0.0037	0.0362	22.692	5.226	-2.567
8	9.4107	-2.2228	-1.2531	9.2045	-1.5548	0.7634	-0.1731	-0.8042	0.1518	0.2533	0.4301	0.7684	0.0609	0.0839	-0.257	0.0853	0.0206	-0.0166	0.1972	-0.0254	0.1056	13.136	-1.093	28.895
9	7.7606	3.6076	-2.1246	10.8121	-3.3071	1.396	-0.2422	0.5209	-0.0564	-0.4839	0.2862	0.2703	0.2831	-0.1029	-0.044	0.1303	-0.001	0.0055	0.0707	-0.0176	0.0255	20.292	-6.516	-3.705
10	12.55	0.5163	-4.8036	5.007	0.8208	2.588	0.2006	-0.7002	-0.0344	0.127	-0.2172	-0.1718	0.0789	0.2629	0.0166	0.0812	-0.0043	-0.0088	0.0739	0.027	0.0246	24.554	-4.086	29.899
11	8.3842	-0.7552	0.444	1.9427	-3.7133	7.2769	0.4393	0.2304	-0.7778	-0.579	-0.1432	0.1456	1.1345	0.1562	-0.2961	0.2652	0.0099	-0.1575	0.0701	0.0238	0.2084	13.198	-11.458	9.977
12	9.899	3.3551	1.9879	2.3725	1.126	6.976	0.0105	-0.1558	-0.5383	0.2874	0.0869	-0.2458	0.246	0.4361	-0.0975	0.0777	0.0515	-0.0259	0.0573	-0.0117	0.0623	32.814	-0.217	16.118
13	1.1659	0.6832	-0.9751	0.6681	-1.2949	2.7722	-0.1717	0.073	-0.0357	-0.112	0.0615	-0.0567	0.1797	-0.1107	0.1102	0.0751	0.0011	-0.0293	0.0249	-0.0313	0.1191	20.766	-1.474	6.251
14	4.0326	0.2752	-2.6351	0.3566	0.0617	2.5919	-0.0864	-0.2336	-0.3087	-0.0375	-0.124	-0.0035	0.0434	0.2019	0.2103	0.0591	0.0255	-0.0364	0.0738	-0.0051	0.1035	20.294	-1.683	19.843
15	10.2062	-2.9323	4.6585	9.6279	3.1971	4.4714	0.1203	0.5937	0.1186	-0.3353	0.0759	-0.481	-0.092	0.4021	-0.1962	0.0445	-0.0126	0.0105	0.081	-0.0138	0.0725	30.727	7.26	3.227
16	4.5345	-2.3172	3.8497	10.0669	-0.1683	3.7461	0.2063	-0.2649	-0.2945	0.2835	0.0893	0.3146	0.254	-0.2171	-0.2956	0.0381	-0.02	0.0051	0.0437	0.0112	0.0932	7.702	-6.059	22.791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 21
2	X-RAY DIFFRACTION	2	B	3 - 21
3	X-RAY DIFFRACTION	3	A	22 - 32
4	X-RAY DIFFRACTION	4	B	22 - 32
5	X-RAY DIFFRACTION	5	A	33 - 42
6	X-RAY DIFFRACTION	6	B	33 - 42
7	X-RAY DIFFRACTION	7	A	43 - 51
8	X-RAY DIFFRACTION	8	B	43 - 51
9	X-RAY DIFFRACTION	9	A	52 - 65
10	X-RAY DIFFRACTION	10	B	52 - 65
11	X-RAY DIFFRACTION	11	A	66 - 73
12	X-RAY DIFFRACTION	12	B	66 - 73
13	X-RAY DIFFRACTION	13	A	74 - 86
14	X-RAY DIFFRACTION	14	B	74 - 86
15	X-RAY DIFFRACTION	15	A	87 - 94
16	X-RAY DIFFRACTION	16	B	87 - 94

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