PDB-3soy: Nuclear transport factor 2 (NTF2-like) superfamily protein from S...

ID or keywords:

Entry

Database: PDB / ID: 3soy

Title

Nuclear transport factor 2 (NTF2-like) superfamily protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Components

NTF2-like superfamily protein

Keywords

MEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / putative outer membrane protein / Secreted Effector Proteins / Program for the Characterization of Secreted Effector Proteins / PCSEP

Function / homology

Function and homology information

Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / 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

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Cuff, M.E. / Li, H. / Jedrzejczak, R. / Brown, R.N. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)

Citation

Journal: TO BE PUBLISHED
Title: Nuclear transport factor 2 (NTF2-like) superfamily protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Authors: Cuff, M.E. / Li, H. / Jedrzejczak, R. / Brown, R.N. / Adkins, J.N. / Joachimiak, A.

History

Deposition	Jun 30, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3soy.cif.gz	73.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3soy.ent.gz	56.8 KB	Display	PDB format
PDBx/mmJSON format	3soy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3soy_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	3soy_full_validation.pdf.gz	449.6 KB	Display
Data in XML	3soy_validation.xml.gz	8.6 KB	Display
Data in CIF	3soy_validation.cif.gz	11.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/so/3soy ftp://data.pdbj.org/pub/pdb/validation_reports/so/3soy	HTTPS FTP

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Related structure data

Similar structure data	5w0x-d 6np1-d 5cxz-d 4enx-d 5dsh-d 3hx8-1 3tca-1 6o5u-d 6bc5-d 4gn1-2 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: APC101574

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: NTF2-like superfamily protein

hetero molecules

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

1

A: NTF2-like superfamily protein

hetero molecules

A: NTF2-like superfamily protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	79.346, 79.346, 107.293
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Details

likely dimer: x,y,z and x,-y+1/2,-z+1/4

#1: Protein	NTF2-like superfamily protein / Putative outer membrane protein Mass: 16280.913 Da / Num. of mol.: 1 / Fragment: residues 39-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: STM1528 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8ZPH9
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.59 Å³/Da / Density % sol: 52.57 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1M Sodium Malonate pH 7.0, 0.1M HEPES:NaOH pH 7.0, 0.5% Jeffamine ED-2001 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97931, 0.97918

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2011

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97931	1
2	0.97918	1

Reflection

Redundancy: 13.3 % / Av σ(I) over netI: 44.66 / Number: 150954 / R_merge(I) obs: 0.079 / Χ²: 1.46 / D res high: 2 Å / D res low: 50 Å / Num. obs: 11364 / % possible obs: 95.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.43	50	96.9	1	0.06	5.183	11.8
4.31	5.43	99.8	1	0.056	3.638	13.2
3.76	4.31	100	1	0.06	3.202	13.5
3.42	3.76	99.8	1	0.062	2.258	14
3.17	3.42	100	1	0.067	1.542	14.3
2.99	3.17	100	1	0.079	1.267	14.2
2.84	2.99	100	1	0.101	1.109	14.3
2.71	2.84	100	1	0.116	0.995	14.4
2.61	2.71	100	1	0.146	0.895	14.4
2.52	2.61	100	1	0.184	0.837	14.4
2.44	2.52	100	1	0.218	0.82	14.5
2.37	2.44	100	1	0.299	0.797	13.9
2.31	2.37	99.1	1	0.359	0.78	13.7
2.25	2.31	95.7	1	0.39	0.725	13.4
2.2	2.25	92.6	1	0.469	0.707	13.2
2.15	2.2	89.4	1	0.442	0.72	13.3
2.11	2.15	87.5	1	0.509	0.664	12.8
2.07	2.11	84.9	1	0.551	0.646	11.7
2.03	2.07	81.3	1	0.703	0.658	10.3
2	2.03	78.3	1	0.787	0.631	8.5

Reflection

Resolution: 2→56.11 Å / Num. all: 11364 / Num. obs: 11364 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / R_merge(I) obs: 0.079 / Net I/σ(I): 8.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2-2.03	8.5	0.787	1	78.3
2.03-2.07	10.3	0.703	1	81.3
2.07-2.11	11.7	0.551	1	84.9
2.11-2.15	12.8	0.509	1	87.5
2.15-2.2	13.3	0.442	1	89.4
2.2-2.25	13.2	0.469	1	92.6
2.25-2.31	13.4	0.39	1	95.7
2.31-2.37	13.7	0.359	1	99.1
2.37-2.44	13.9	0.299	1	100
2.44-2.52	14.5	0.218	1	100
2.52-2.61	14.4	0.184	1	100
2.61-2.71	14.4	0.146	1	100
2.71-2.84	14.4	0.116	1	100
2.84-2.99	14.3	0.101	1	100
2.99-3.17	14.2	0.079	1	100
3.17-3.42	14.3	0.067	1	100
3.42-3.76	14	0.062	1	99.8
3.76-4.31	13.5	0.06	1	100
4.31-5.43	13.2	0.056	1	99.8
5.43-50	11.8	0.06	1	96.9

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.1 Å / D res low: 50 Å / FOM : 0.269 / FOM acentric: 0.293 / FOM centric: 0.128 / Reflection: 10072 / Reflection acentric: 8596 / Reflection centric: 1476

Phasing MAD set

Highest resolution: 2.1 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.77	1	0.1	0.1	0	0	8596	1476
2	0.98	0.95	19.4	27.1	0.27	0.24	6586	1255

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.98-50	2.1	1	0.8	0.4	0	0	22	25
1	7.46-12.98	1.18	1	0.5	0.4	0	0	133	75
1	5.23-7.46	1.72	1	0.5	0.3	0	0	342	126
1	4.03-5.23	1.13	1	0.3	0.2	0	0	645	172
1	3.28-4.03	1.36	1	0.2	0.1	0	0	1058	219
1	2.76-3.28	3.14	1	0.1	0	0	0	1552	263
1	2.39-2.76	9.1	1	0.1	0	0	0	2162	305
1	2.1-2.39	2.32	1	0	0	0	0	2682	291
2	12.98-50	0.94	0.87	39	50.3	0.76	0.45	22	22
2	7.46-12.98	0.95	0.93	31.9	42.8	0.72	0.46	133	74
2	5.23-7.46	0.96	0.9	28.2	34.5	0.62	0.46	342	126
2	4.03-5.23	0.98	0.94	30.3	38.7	0.38	0.26	645	172
2	3.28-4.03	0.99	0.97	25	29.7	0.27	0.19	1058	219
2	2.76-3.28	0.99	0.97	16.2	20.1	0.23	0.15	1552	263
2	2.39-2.76	1	0.99	14.4	17.6	0.13	0.09	2160	299
2	2.1-2.39	1	1	16.2	20.4	0.07	0.05	674	80

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	49.4076	0.73	0.074	0.068	6.34	0
2	69.4369	0.731	0.073	0.067	4.089	-0.174

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.98-50	0.453	0.652	0.277	47	22	25
7.46-12.98	0.528	0.671	0.274	208	133	75
5.23-7.46	0.569	0.661	0.316	468	342	126
4.03-5.23	0.506	0.583	0.218	817	645	172
3.28-4.03	0.464	0.53	0.144	1277	1058	219
2.76-3.28	0.334	0.37	0.122	1815	1552	263
2.39-2.76	0.191	0.209	0.059	2467	2162	305
2.1-2.39	0.075	0.083	0.007	2973	2682	291

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 11352

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.92-100	53	0.845	503
4.66-5.92	46.9	0.929	505
4.06-4.66	53.2	0.921	512
3.67-4.06	55.1	0.914	512
3.39-3.67	50.5	0.911	503
3.19-3.39	59	0.89	511
3.02-3.19	65	0.838	511
2.89-3.02	65.7	0.788	506
2.77-2.89	71	0.788	502
2.68-2.77	67.3	0.791	506
2.59-2.68	73.2	0.758	501
2.52-2.59	70.5	0.744	502
2.45-2.52	78.1	0.748	507
2.39-2.45	83.1	0.753	505
2.33-2.39	82.5	0.747	501
2.28-2.33	87.7	0.737	508
2.23-2.28	80.9	0.787	509
2.18-2.23	79.9	0.798	503
2.14-2.18	85.9	0.803	506
2.1-2.14	83.4	0.821	502
2.06-2.1	86.8	0.814	511
2-2.06	87.8	0.648	726

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2→56.11 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.968 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.159 / SU ML: 0.158 / SU R Cruickshank DPI: 0.1649 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22085	537	4.7 %	RANDOM
R_work	0.17579	-	-	-
obs	0.17795	10779	95.03 %	-
all	-	11316	-	-

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: 45.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.64 Å²	0 Å²	0 Å²
2-	-	-2.64 Å²	0 Å²
3-	-	-	5.27 Å²

Refinement step

Cycle: LAST / Resolution: 2→56.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1127	0	18	71	1216

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.021	1177
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	792
X-RAY DIFFRACTION	r_angle_refined_deg	1.742	1.918	1597
X-RAY DIFFRACTION	r_angle_other_deg	0.966	3	1905
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.417	5	141
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.075	22.857	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.719	15	175
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.115	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	165
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	1327
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	263
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	0.712	1.5	703
X-RAY DIFFRACTION	r_mcbond_other	0.192	1.5	290
X-RAY DIFFRACTION	r_mcangle_it	1.361	2	1134
X-RAY DIFFRACTION	r_scbond_it	2.327	3	474
X-RAY DIFFRACTION	r_scangle_it	3.806	4.5	463
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.001→2.053 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	26	-
R_work	0.299	652	-
obs	-	-	78.29 %

Refinement TLS params.

Method: refined / Origin x: 51.2227 Å / Origin y: 9.6149 Å / Origin z: 10.5118 Å

	11	12	13	21	22	23	31	32	33
T	0.128 Å²	-0.0542 Å²	0.1202 Å²	-	0.0985 Å²	-0.1132 Å²	-	-	0.2322 Å²
L	1.1029 °²	0.1879 °²	-0.0673 °²	-	2.7642 °²	0.9705 °²	-	-	2.4508 °²
S	-0.1954 Å °	0.0616 Å °	-0.2128 Å °	0.0831 Å °	-0.1608 Å °	-0.1404 Å °	0.3389 Å °	-0.2073 Å °	0.3562 Å °

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