PDB-3blz: Crystal structure of a ntf2-like protein of unknown function (sba...

ID or keywords:

Entry

Database: PDB / ID: 3blz

Title

Crystal structure of a ntf2-like protein of unknown function (sbal_0622) from shewanella baltica os155 at 1.75 A resolution

Components

NTF2-like protein of unknown function

Keywords

UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Putative lumazine-binding / Putative lumazine-binding / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein

Function and homology information

Biological species

Shewanella baltica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.75 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of a NTF2-like protein of unknown function (YP_001049020.1) from Shewanella baltica OS155 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Dec 11, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3blz.cif.gz	322.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3blz.ent.gz	268.7 KB	Display	PDB format
PDBx/mmJSON format	3blz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3blz_validation.pdf.gz	535.7 KB	Display	wwPDB validaton report
Full document	3blz_full_validation.pdf.gz	544.3 KB	Display
Data in XML	3blz_validation.xml.gz	67 KB	Display
Data in CIF	3blz_validation.cif.gz	93.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/3blz ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blz	HTTPS FTP

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Related structure data

Similar structure data	6kn1-d 1i51-d 6t3v-d 5kct-d 3r7b-d 5dxm-d 5krj-d 2fqq-1 5tmq-d 5tlf-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 - HomologyF&H Search
Other databases	TargetDB: 378217

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: NTF2-like protein of unknown function

B: NTF2-like protein of unknown function

C: NTF2-like protein of unknown function

D: NTF2-like protein of unknown function

E: NTF2-like protein of unknown function

F: NTF2-like protein of unknown function

G: NTF2-like protein of unknown function

H: NTF2-like protein of unknown function

I: NTF2-like protein of unknown function

J: NTF2-like protein of unknown function

K: NTF2-like protein of unknown function

L: NTF2-like protein of unknown function

hetero molecules

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

1

A: NTF2-like protein of unknown function

B: NTF2-like protein of unknown function

C: NTF2-like protein of unknown function

D: NTF2-like protein of unknown function

hetero molecules

defined by software
56.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: NTF2-like protein of unknown function

F: NTF2-like protein of unknown function

G: NTF2-like protein of unknown function

H: NTF2-like protein of unknown function

hetero molecules

defined by software
57 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: NTF2-like protein of unknown function

J: NTF2-like protein of unknown function

K: NTF2-like protein of unknown function

L: NTF2-like protein of unknown function

hetero molecules

defined by software
56.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.085, 58.121, 140.462
Angle α, β, γ (deg.)	80.930, 78.430, 60.600
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASN / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 3 - 125 / Label seq-ID: 4 - 126

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J
11	K	K
12	L	L

#1: Protein	NTF2-like protein of unknown function Mass: 14062.471 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / Gene: YP_001049020.1, Sbal_0622 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3D088
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1158 / 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: 2.35 Å³/Da / Density % sol: 47.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: NANODROP, 20.0% 2-propanol, 20.0% PEG 4000, 0.1M Citric acid pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1.0000, 0.9796

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.9796	1

Reflection

Resolution: 1.75→29.348 Å / Num. obs: 126809 / % possible obs: 81.7 % / Redundancy: 1.9 % / R_merge(I) obs: 0.042 / R_sym value: 0.042 / Net I/σ(I): 11.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.75-1.8	1.9	0.456	1.5	8054	4345	0.456	37.8
1.8-1.84	1.9	0.356	1.9	9851	5254	0.356	46.6
1.84-1.9	1.9	0.289	2.3	11717	6239	0.289	57.6
1.9-1.96	1.8	0.213	3.3	14039	7661	0.213	72.5
1.96-2.02	1.8	0.165	4.3	17406	9434	0.165	92
2.02-2.09	1.9	0.14	5	17884	9190	0.14	92.8
2.09-2.17	1.9	0.108	6.6	17319	8893	0.108	92.7
2.17-2.26	1.9	0.086	8.2	16610	8545	0.086	93.1
2.26-2.36	1.9	0.077	9.2	15943	8192	0.077	93
2.36-2.47	1.9	0.064	10.8	15352	7882	0.064	93.2
2.47-2.61	1.9	0.058	11.5	14514	7464	0.058	93.1
2.61-2.77	1.9	0.047	9.8	13808	7086	0.047	93.1
2.77-2.96	1.9	0.038	16.2	12787	6594	0.038	93.4
2.96-3.2	1.9	0.033	19.4	12002	6217	0.033	93.1
3.2-3.5	1.9	0.028	20.8	10872	5665	0.028	93.1
3.5-3.91	1.9	0.026	20.6	9818	5128	0.026	92.8
3.91-4.52	1.9	0.024	23.3	8416	4496	0.024	92.5
4.52-5.53	1.7	0.024	21.2	6661	3815	0.024	93
5.53-7.83	1.9	0.023	24.2	5919	3050	0.023	96.5
7.83-29.348	2	0.019	26	3296	1659	0.019	94.8

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SOLVE		phasing
MolProbity	3beta29	model building
SCALA		data scaling
PDB_EXTRACT	3	data extraction
ADSC	Quantum	data collection
MOSFLM		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.75→29.348 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.953 / SU B: 4.559 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.194	6400	5 %	RANDOM
R_work	0.152	-	-	-
obs	0.154	126808	81.57 %	-

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: 16.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	-0.23 Å²	-0.31 Å²
2-	-	0.22 Å²	1.05 Å²
3-	-	-	-0.39 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→29.348 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11418	0	126	1158	12702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	12337
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8137
X-RAY DIFFRACTION	r_angle_refined_deg	1.446	1.932	16799
X-RAY DIFFRACTION	r_angle_other_deg	0.934	3	19863
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.463	5	1585
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.227	23.829	538
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.602	15	1905
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.974	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1884
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	14069
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2622
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	2242
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	8255
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	6037
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	6214
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	965
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.156	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.272	0.2	38
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.146	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.946	3	8454
X-RAY DIFFRACTION	r_mcbond_other	0.667	3	3116
X-RAY DIFFRACTION	r_mcangle_it	2.55	5	12566
X-RAY DIFFRACTION	r_scbond_it	4.304	8	5106
X-RAY DIFFRACTION	r_scangle_it	5.753	11	4233

Refine LS restraints NCS

Ens-ID: 1 / Number: 1377 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	MEDIUM POSITIONAL	0.18	0.5
2	B	MEDIUM POSITIONAL	0.18	0.5
3	C	MEDIUM POSITIONAL	0.18	0.5
4	D	MEDIUM POSITIONAL	0.23	0.5
5	E	MEDIUM POSITIONAL	0.23	0.5
6	F	MEDIUM POSITIONAL	0.19	0.5
7	G	MEDIUM POSITIONAL	0.34	0.5
8	H	MEDIUM POSITIONAL	0.22	0.5
9	I	MEDIUM POSITIONAL	0.23	0.5
10	J	MEDIUM POSITIONAL	0.22	0.5
11	K	MEDIUM POSITIONAL	0.18	0.5
12	L	MEDIUM POSITIONAL	0.22	0.5
1	A	MEDIUM THERMAL	0.9	2
2	B	MEDIUM THERMAL	0.92	2
3	C	MEDIUM THERMAL	1.01	2
4	D	MEDIUM THERMAL	0.9	2
5	E	MEDIUM THERMAL	0.92	2
6	F	MEDIUM THERMAL	0.83	2
7	G	MEDIUM THERMAL	0.89	2
8	H	MEDIUM THERMAL	0.91	2
9	I	MEDIUM THERMAL	0.95	2
10	J	MEDIUM THERMAL	0.89	2
11	K	MEDIUM THERMAL	0.88	2
12	L	MEDIUM THERMAL	0.85	2

LS refinement shell

Resolution: 1.75→1.79 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	215	-
R_work	0.242	4013	-
all	-	4228	-
obs	-	-	36.79 %

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	0.8216	0.5642	-0.3879	1.3146	-0.1932	1.2024	-0.0403	0.1396	0.0659	-0.1555	0.0905	0.0022	-0.1325	0.0779	-0.0502	-0.0337	-0.0636	0.0231	-0.0705	-0.0024	-0.0569	52.9691	6.7327	71.455
2	1.0354	0.3041	-0.0264	1.6708	-0.1194	1.1786	0.14	-0.0884	0.1087	0.3147	-0.0738	0.1467	-0.2012	-0.0152	-0.0662	0.0235	-0.0677	0.0577	-0.1063	-0.0294	-0.0395	46.7799	8.7735	91.5981
3	0.8073	0.364	-0.0692	1.5128	-0.433	1.074	0.0357	-0.0613	0.0064	0.1545	-0.004	0.0464	0.1407	-0.0819	-0.0317	-0.0164	-0.0623	-0.013	-0.0973	0.0072	-0.0711	38.6413	-17.7624	89.2009
4	0.546	0.3006	-0.0099	1.1807	-0.1637	1.4927	-0.0552	0.1775	0.0688	-0.1983	0.14	0.1866	0.1393	-0.2741	-0.0848	-0.0296	-0.0965	-0.0514	-0.0249	0.0389	-0.0242	32.3331	-12.0349	69.6743
5	1.6277	-0.0358	-0.2851	0.6094	-0.0184	1.697	0.0864	0.2338	-0.0594	-0.1071	-0.049	-0.065	0.1204	0.1577	-0.0374	-0.0984	0.038	0.0021	0.0483	-0.0264	-0.0633	68.0013	4.2692	24.0535
6	1.801	0.0861	0.0027	0.4473	-0.2451	1.1252	0.0941	-0.2493	0.0815	0.0383	-0.067	0.0126	-0.0489	0.1636	-0.0271	-0.1185	-0.0206	0.0031	0.0467	-0.0234	-0.0632	68.4846	9.3855	44.801
7	1.7141	0.0864	-0.4408	0.4577	-0.2752	1.2474	0.0777	-0.1518	-0.0536	0.0289	0.0053	-0.0015	0.0419	-0.1368	-0.083	-0.1173	-0.0155	-0.011	0.0259	0.0398	-0.0544	41.2585	3.3815	44.2302
8	1.7738	-0.2187	0.0825	0.6568	-0.4695	1.3977	0.1163	0.2732	0.1122	-0.0575	0.0032	0.0908	-0.0779	-0.1877	-0.1196	-0.1012	0.0355	0.0076	0.0625	0.0594	-0.0429	41.3948	12.7649	25.0826
9	1.2499	-0.7795	0.1902	1.7937	-0.119	2.1637	0.2	0.1116	-0.2427	-0.4197	-0.0935	0.2932	0.457	-0.008	-0.1065	0.1415	0.0614	-0.0942	-0.1111	-0.0326	0.0007	45.5347	6.86	-22.5086
10	1.0467	-0.9351	0.412	1.902	-0.5341	1.4083	-0.1005	-0.1546	-0.1054	0.1391	0.1484	0.1053	0.1961	0.1026	-0.0479	0.0136	0.089	-0.0079	-0.0686	0.002	-0.0613	52.3277	8.4412	-2.3523
11	0.8184	-0.661	0.041	1.7316	-0.0657	1.5836	-0.1356	-0.1903	-0.1093	0.2514	0.2165	0.2384	-0.1421	-0.2749	-0.0809	0.0058	0.0972	0.0542	-0.0312	0.0477	-0.0201	33.5633	29.0444	-0.4331
12	0.8037	-0.6748	-0.0223	1.7864	-0.633	1.4224	0.0805	0.0782	0.0297	-0.232	0.0056	0.0326	-0.1664	-0.0643	-0.086	0.0279	0.0434	0.0185	-0.0916	0.0109	-0.049	39.7107	34.0733	-20.0374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 126	4 - 127
2	X-RAY DIFFRACTION	2	B	B	3 - 126	4 - 127
3	X-RAY DIFFRACTION	3	C	C	3 - 126	4 - 127
4	X-RAY DIFFRACTION	4	D	D	3 - 126	4 - 127
5	X-RAY DIFFRACTION	5	E	E	3 - 126	4 - 127
6	X-RAY DIFFRACTION	6	F	F	3 - 125	4 - 126
7	X-RAY DIFFRACTION	7	G	G	3 - 126	4 - 127
8	X-RAY DIFFRACTION	8	H	H	3 - 125	4 - 126
9	X-RAY DIFFRACTION	9	I	I	3 - 125	4 - 126
10	X-RAY DIFFRACTION	10	J	J	3 - 126	4 - 127
11	X-RAY DIFFRACTION	11	K	K	3 - 125	4 - 126
12	X-RAY DIFFRACTION	12	L	L	3 - 125	4 - 126

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