PDB-3fka: CRYSTAL STRUCTURE OF A NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (SP...

ID or keywords:

Entry

Database: PDB / ID: 3fka

Title

CRYSTAL STRUCTURE OF A NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (SPO1084) FROM SILICIBACTER POMEROYI DSS-3 AT 1.69 A RESOLUTION

Components

uncharacterized NTF-2 like protein

Keywords

UNKNOWN FUNCTION / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2

Function / homology

Function and homology information

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
Similarity search - Domain/homology

Biological species

Silicibacter pomeroyi DSS-3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.69 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of NTF-2 like protein of unknown function (YP_166335.1) from SILICIBACTER POMEROYI DSS-3 at 1.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Dec 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 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	Feb 1, 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
Revision 1.5	Oct 16, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3fka.cif.gz	128.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3fka.ent.gz	101 KB	Display	PDB format
PDBx/mmJSON format	3fka.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3fka_validation.pdf.gz	482.7 KB	Display	wwPDB validaton report
Full document	3fka_full_validation.pdf.gz	496.2 KB	Display
Data in XML	3fka_validation.xml.gz	28 KB	Display
Data in CIF	3fka_validation.cif.gz	40.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fk/3fka ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fka	HTTPS FTP

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Related structure data

Similar structure data	3p4u-d 3v6l-d 1jxq-1 4rsw-d 1ue7-1 4le6-3 3e29-d 1j9k-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 391417

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: uncharacterized NTF-2 like protein

B: uncharacterized NTF-2 like protein

C: uncharacterized NTF-2 like protein

D: uncharacterized NTF-2 like protein

hetero molecules

55.9 kDa, 4 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)	52.424, 92.002, 120.072
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

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	MSE	MSE	GLU	GLU	6	A	A	1 - 5	2 - 6
2	1	MSE	MSE	GLU	GLU	6	B	B	1 - 5	2 - 6
3	1	MSE	MSE	GLU	GLU	6	C	C	1 - 5	2 - 6
4	1	MSE	MSE	GLU	GLU	6	D	D	1 - 5	2 - 6
1	2	HIS	HIS	ARG	ARG	4	A	A	6 - 119	7 - 120
2	2	HIS	HIS	ARG	ARG	4	B	B	6 - 119	7 - 120
3	2	HIS	HIS	ARG	ARG	4	C	C	6 - 119	7 - 120
4	2	HIS	HIS	ARG	ARG	4	D	D	6 - 119	7 - 120

#1: Protein	uncharacterized NTF-2 like protein Mass: 13811.646 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Gene: SPO1084, YP_166335.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LUH0
#2: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 9 / Source method: obtained synthetically
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.06 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.94645,0.97967

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.94645	1
2	0.97967	1

Reflection

Resolution: 1.69→29.961 Å / Num. obs: 62487 / % possible obs: 95.2 % / Redundancy: 3.7 % / B_iso Wilson estimate: 18.182 Å² / R_merge(I) obs: 0.08 / R_rim(I) all: 0.093 / R_sym value: 0.08 / Net I/av σ(I): 7.017 / Net I/σ(I): 11 / Num. measured all: 231193

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.69-1.73	3.4	0.629	1.2	11241	3354	0.744	0.629	1.9	71.2
1.73-1.78	3.5	0.523	1.5	14122	4047	0.614	0.523	2.4	88
1.78-1.83	3.8	0.415	1.8	16502	4396	0.484	0.415	3.1	96.5
1.83-1.89	3.8	0.327	2.3	16195	4293	0.38	0.327	3.8	96.9
1.89-1.95	3.8	0.237	3.2	15798	4165	0.277	0.237	5.2	96.8
1.95-2.02	3.8	0.186	4	15332	4039	0.217	0.186	6.3	96.8
2.02-2.1	3.8	0.153	4.9	14755	3895	0.178	0.153	7.5	97.2
2.1-2.18	3.8	0.129	5.8	14269	3774	0.15	0.129	8.9	97.6
2.18-2.28	3.8	0.118	6.1	13766	3638	0.137	0.118	10	97.8
2.28-2.39	3.8	0.116	6.1	13157	3497	0.135	0.116	11.1	98.1
2.39-2.52	3.8	0.095	7.4	12526	3327	0.11	0.095	12.5	98.4
2.52-2.67	3.8	0.078	8.9	11883	3164	0.091	0.078	14.4	98.6
2.67-2.86	3.7	0.068	9.9	11242	3005	0.079	0.068	15.7	98.8
2.86-3.09	3.7	0.062	10.5	10357	2782	0.072	0.062	18.3	98
3.09-3.38	3.7	0.057	10.7	9576	2576	0.067	0.057	20.7	99.2
3.38-3.78	3.7	0.046	12.9	8744	2372	0.054	0.046	24	98.9
3.78-4.36	3.7	0.044	13.8	7716	2108	0.051	0.044	25.2	99.4
4.36-5.34	3.6	0.043	14.3	6483	1797	0.05	0.043	26.7	99.4
5.34-7.56	3.5	0.048	13.4	4968	1436	0.056	0.048	24.9	99.6
7.56-29.96	3.1	0.047	10.9	2561	822	0.056	0.047	25.6	97.9

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
SCALA	3.2.5	data scaling
PDB_EXTRACT	3.006	data extraction
MOSFLM		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.69→29.961 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.95 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.749 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.098
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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	0.2	3170	5.1 %	RANDOM
R_work	0.179	59260	-	-
obs	0.181	62430	94.86 %	-

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 max: 63.14 Å² / B_iso mean: 27.137 Å² / B_iso min: 11.47 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	0 Å²	0 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	0.55 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→29.961 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3756	0	76	508	4340

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4223
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	2812
X-RAY DIFFRACTION	r_angle_refined_deg	1.917	1.942	5800
X-RAY DIFFRACTION	r_angle_other_deg	1.667	3	6867
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.931	5	574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.041	22.865	192
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.571	15	729
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.18	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	659
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4814
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	937
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.3	736
X-RAY DIFFRACTION	r_nbd_other	0.162	0.3	2972
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.5	1960
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.5	2265
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.5	678
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.133	0.3	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.211	0.3	68
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.185	0.5	63
X-RAY DIFFRACTION	r_mcbond_it	0.859	2	2827
X-RAY DIFFRACTION	r_mcbond_other	0.182	2	1032
X-RAY DIFFRACTION	r_mcangle_it	1.171	3	4163
X-RAY DIFFRACTION	r_scbond_it	0.708	2	1857
X-RAY DIFFRACTION	r_scangle_it	1.022	3	1582

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	A	1257	MEDIUM POSITIONAL	0.31	0.5
2	B	1257	MEDIUM POSITIONAL	0.42	0.5
3	C	1257	MEDIUM POSITIONAL	0.31	0.5
4	D	1257	MEDIUM POSITIONAL	0.3	0.5
1	A	48	LOOSE POSITIONAL	0.85	5
2	B	48	LOOSE POSITIONAL	1.15	5
3	C	48	LOOSE POSITIONAL	1.07	5
4	D	48	LOOSE POSITIONAL	0.79	5
1	A	1257	MEDIUM THERMAL	0.84	2
2	B	1257	MEDIUM THERMAL	0.81	2
3	C	1257	MEDIUM THERMAL	0.61	2
4	D	1257	MEDIUM THERMAL	0.86	2
1	A	48	LOOSE THERMAL	4.18	10
2	B	48	LOOSE THERMAL	2.44	10
3	C	48	LOOSE THERMAL	1.47	10
4	D	48	LOOSE THERMAL	1.15	10

LS refinement shell

Resolution: 1.69→1.734 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	172	-
R_work	0.258	3179	-
all	-	3351	-
obs	-	-	69.97 %

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	1.3474	0.0643	0.1822	0.2431	-0.2721	1.0184	-0.0129	-0.0133	0.025	0.033	0.0173	-0.0969	0.0031	0.0179	-0.0044	-0.1605	-0.0034	0.0022	-0.1836	-0.0087	-0.1448	22.52	65.58	17.422
2	1.3268	-0.1338	0.5429	0.758	-0.1066	1.0609	0.0097	0.0559	-0.0551	-0.0044	0.0347	0.0236	0.0484	-0.0883	-0.0444	-0.1741	-0.0019	0.0088	-0.1721	0.007	-0.1628	1.448	64.562	12.965
3	1.6322	-0.4038	-0.1797	2.7012	-0.5704	0.9316	-0.0949	-0.2389	0.0343	0.4541	0.1507	0.1302	-0.1321	-0.0992	-0.0558	-0.0601	0.0131	0.0192	-0.1376	0.0231	-0.1168	5.539	48.217	38.916
4	1.1164	-0.6346	-0.3291	2.1693	-0.7859	0.9128	-0.0199	0.1163	-0.1384	-0.2274	0.0277	0.0068	0.1399	-0.0055	-0.0078	-0.1092	-0.0081	-0.022	-0.1419	0.0038	-0.1283	14.155	36.339	22.998

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 119
2	X-RAY DIFFRACTION	2	B	0 - 119
3	X-RAY DIFFRACTION	3	C	1 - 119
4	X-RAY DIFFRACTION	4	D	1 - 119

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