PDB-1ojh: Crystal structure of NblA from PCC 7120

ID or keywords:

Entry

Database: PDB / ID: 1ojh

Title

Crystal structure of NblA from PCC 7120

Components

NBLA

Keywords

PROTEIN BINDING / DEGRADATION PROTEIN / PHYCOBILISOME DEGRADATION

Function / homology

Phycobilisome degradation protein NblA / Phycobilisome degradation protein NblA / Phycobilisome degradation protein NblA superfamily / Phycobilisome degradation protein nblA / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / NblA protein

Function and homology information

Biological species

ANABAENA SP. PCC 7120 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Bienert, R. / Baier, K. / Lockau, W. / Heinemann, U.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of Nbla from Anabaena Sp. Pcc 7120, a Small Protein Playing a Key Role in Phycobilisome Degradation.
Authors: Bienert, R. / Baier, K. / Volkmer, R. / Lockau, W. / Heinemann, U.

History

Deposition	Jul 10, 2003	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 15, 2004	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 3, 2011	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.3	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site 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_conn.pdbx_leaving_atom_flag / _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	1ojh.cif.gz	146.5 KB	Display	PDBx/mmCIF format
PDB format	pdb1ojh.ent.gz	120.4 KB	Display	PDB format
PDBx/mmJSON format	1ojh.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/oj/1ojh ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NBLA

B: NBLA

C: NBLA

D: NBLA

E: NBLA

F: NBLA

G: NBLA

H: NBLA

I: NBLA

J: NBLA

K: NBLA

L: NBLA

hetero molecules

92.4 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NBLA

B: NBLA

hetero molecules

defined by author&software
15.5 kDa, 2 polymers

2

C: NBLA

D: NBLA

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

3

E: NBLA

F: NBLA

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

4

G: NBLA

H: NBLA

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

5

I: NBLA

J: NBLA

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

6

K: NBLA

L: NBLA

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

Unit cell

Length a, b, c (Å)	43.176, 95.918, 104.835
Angle α, β, γ (deg.)	90.00, 97.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	NBLA / PHYCOBILISOME DEGRADATION PROTEIN HOMOLOGUE Mass: 7690.148 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. PCC 7120 (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8YNP7
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.3 Å³/Da / Density % sol: 47 %
Crystal grow	pH: 8.5 Details: 100 MM TRIS/HCL PH 8.5 10% PEG2000, 100 MM MGCL2, 15% ETHYLENGLYCOL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
Detector	Type: ADSC CCD / Detector: CCD / Date: May 15, 2002 / Details: TOROIDAL MIRROR
Radiation	Monochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9393 Å / Relative weight: 1
Reflection	Resolution: 1.8→20 Å / Num. obs: 74292 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / R_merge(I) obs: 0.069 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.8→1.97 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
XDS		data reduction
XSCALE		data scaling
SOLVE	V. 2.03	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→20 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.949 / SU B: 2.531 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / 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	3874	5 %	RANDOM
R_work	0.182	-	-	-
obs	0.184	74292	99.7 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	1.55 Å²
2-	-	1.09 Å²	0 Å²
3-	-	-	-0.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5108	0	8	254	5370

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	5270
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	4661
X-RAY DIFFRACTION	r_angle_refined_deg	1.478	1.933	7066
X-RAY DIFFRACTION	r_angle_other_deg	1.515	3	10892
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.567	5	607
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	780
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5727
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1052
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.12	1094
X-RAY DIFFRACTION	r_nbd_other	0.212	0.12	4919
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.092	0.2	2995
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.12	209
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	0.158	0.12	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.23	0.12	185
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.176	0.12	23
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	3.813	4	3085
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	6.349	8	4968
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	7.144	8	2185
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	10.578	12	2098
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

LS refinement shell

Resolution: 1.8→1.86 Å / Total num. of bins used: 15 /

	R_factor	Num. reflection
R_free	0.303	346
R_work	0.257	7185

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	4.8017	0.5139	1.5297	0.7354	-0.1447	4.5795	-0.1417	1.08	0.3935	-0.1115	0.0416	0.0362	-0.2567	0.3396	0.1001	0.1666	0.0017	-0.0502	0.3297	0.066	0.1991	0.0124	27.2117	38.6898
2	5.31	1.9172	-1.6759	2.0032	0.1817	1.5931	-0.1976	0.9609	-0.4589	0.0318	0.0358	-0.183	0.0836	0.0195	0.1618	0.1254	-0.0068	-0.0321	0.3707	0.0074	0.178	-2.9305	22.2921	36.7185
3	8.4973	2.9803	-2.5977	0.7181	-0.4981	2.7061	-0.0385	0.5969	0.239	0.0079	0.0759	0.1295	-0.2824	-0.0295	-0.0375	0.1536	-0.0053	-0.0555	0.2345	0.0659	0.2153	-2.5059	27.9268	44.0968
4	2.3392	0.5582	-0.2742	5.3631	-1.8262	1.6285	-0.026	0.1441	-0.2164	-0.335	-0.0176	-0.2152	0.2632	0.0046	0.0436	0.1999	-0.0136	0.0118	0.0503	-0.037	0.1393	20.9004	66.0142	42.1659
5	3.6743	-1.0846	-0.2661	2.1651	0.5534	3.2621	-0.0409	0.0012	-0.4681	-0.2451	0.0733	-0.1564	0.2581	-0.1982	-0.0324	0.1658	0.0073	0.0075	0.0771	-0.0019	0.2708	21.5835	65.1501	47.2231
6	7.398	-0.6124	-5.1206	1.7005	0.6672	5.5631	-0.2142	0.399	-0.5224	-0.3136	0.0482	0.1692	0.4314	-0.4096	0.166	0.2305	-0.0325	-0.0261	0.1204	-0.0272	0.1902	14.7317	68.3512	41.6774
7	2.196	0.4649	0.893	2.2545	0.3682	2.1391	-0.1092	0.1406	0.2321	-0.0994	0.0119	0.0198	-0.0926	0.0062	0.0974	0.1554	0.0109	-0.0215	0.1089	0.0056	0.1469	38.3955	97.413	14.4759
8	4.7448	-0.815	-4.7194	1.7431	0.5357	6.2867	0.0974	0.1664	0.3244	-0.2712	0.0255	-0.0967	-0.2815	-0.2062	-0.1229	0.2114	0.0185	0.0031	0.1048	0.0327	0.1561	38.643	98.3573	8.4024
9	3.9669	0.5957	-3.2005	2.989	-0.1205	4.7807	0.0078	-0.1339	0.1726	-0.0308	0.0593	-0.3583	-0.3605	0.1959	-0.0671	0.1678	-0.0111	-0.0275	0.108	0.0164	0.1923	45.0111	97.7757	15.1396
10	2.9694	-0.5241	2.8647	1.1505	-0.6481	6.7283	-0.0695	-1.1256	0.1513	0.2307	0.0404	0.0964	-0.1545	-0.916	0.0291	0.2098	0.0189	-0.017	0.6002	0.0141	0.1913	14.1338	30.261	11.1853
11	7.2781	-1.7659	-4.1789	3.0066	1.7323	7.1153	-0.1736	-0.5977	-0.5453	0.0167	-0.0539	0.263	0.0976	-0.6286	0.2275	0.1285	-0.0146	-0.0332	0.355	0.0777	0.1319	16.9902	25.0844	12.1304
12	10.1434	-2.6468	-3.3545	1.3909	-0.5204	5.2749	-0.1067	-0.3707	0.1791	0.1567	0.1859	-0.1501	-0.2895	-0.5292	-0.0792	0.1413	0.0177	-0.0454	0.3161	0.0242	0.1439	16.731	32.1554	6.0285
13	2.6718	-0.5241	-1.284	4.1397	1.6455	3.2917	-0.2395	0.118	-0.3915	0.4931	-0.0501	0.0939	0.6777	-0.1056	0.2896	0.2879	-0.0136	0.0562	0.0627	-0.0224	0.1866	38.4076	72.8856	13.15
14	6.3243	1.3042	-0.7263	4.2006	1.3155	5.5215	-0.4277	0.9234	-0.7386	0.3195	0.0967	0.0345	0.7017	-0.1921	0.331	0.2129	-0.0569	0.0506	0.0972	-0.0823	0.2675	37.7802	71.3181	8.2287
15	8.0198	0.0813	-6.5387	1.6442	0.325	5.8672	-0.2464	-0.1314	-0.5035	0.3923	-0.0315	-0.1827	0.3966	0.264	0.2779	0.2271	0.0092	-0.011	0.1004	-0.0202	0.1743	44.7931	75.4398	12.989
16	0.9304	0.1481	0.2106	0.9938	-0.3638	2.3648	-0.0044	-0.0238	0.048	-0.0244	0.0384	0.0193	0.0235	-0.2107	-0.0341	0.1554	0.0283	-0.0012	0.139	0.0262	0.1517	20.9279	90.1538	37.3374
17	5.0169	0.3766	-4.8488	1.2267	-0.0781	5.1758	0.0105	-0.1123	0.1846	0.1394	0.0491	0.1278	-0.1694	0.1452	-0.0596	0.2212	0.0226	-0.0021	0.1278	0.0127	0.1624	20.1466	91.7286	43.4595
18	7.5762	-2.2877	-3.48	3.0734	1.7017	3.0362	-0.0438	0.056	-0.0184	-0.0938	-0.0226	0.3188	0.0176	-0.1513	0.0664	0.1752	0.0092	-0.0228	0.113	0.0204	0.1792	14.3686	90.1683	36.3832

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 25
2	X-RAY DIFFRACTION	1	B	10 - 25
3	X-RAY DIFFRACTION	2	A	26 - 50
4	X-RAY DIFFRACTION	3	B	26 - 50
5	X-RAY DIFFRACTION	4	C	10 - 25
6	X-RAY DIFFRACTION	4	D	10 - 25
7	X-RAY DIFFRACTION	5	C	26 - 50
8	X-RAY DIFFRACTION	6	D	26 - 50
9	X-RAY DIFFRACTION	7	E	10 - 25
10	X-RAY DIFFRACTION	7	F	10 - 25
11	X-RAY DIFFRACTION	8	E	26 - 50
12	X-RAY DIFFRACTION	9	F	26 - 50
13	X-RAY DIFFRACTION	10	G	10 - 25
14	X-RAY DIFFRACTION	10	H	10 - 25
15	X-RAY DIFFRACTION	11	G	26 - 50
16	X-RAY DIFFRACTION	12	H	26 - 50
17	X-RAY DIFFRACTION	13	I	10 - 25
18	X-RAY DIFFRACTION	13	J	10 - 25
19	X-RAY DIFFRACTION	14	I	26 - 50
20	X-RAY DIFFRACTION	15	J	26 - 50
21	X-RAY DIFFRACTION	16	K	10 - 25
22	X-RAY DIFFRACTION	16	L	10 - 25
23	X-RAY DIFFRACTION	17	K	26 - 50
24	X-RAY DIFFRACTION	18	L	26 - 50

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