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- PDB-3en8: Crystal structure of NTF-2 like protein of unknown function (YP_5... -

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Basic information

Entry
Database: PDB / ID: 3en8
TitleCrystal structure of NTF-2 like protein of unknown function (YP_553245.1) from BURKHOLDERIA XENOVORANS LB400 at 1.85 A resolution
Componentsuncharacterized NTF-2 like protein
Keywordsstructural genomics / unknown function / YP_553245.1 / NTF-2 like protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesBurkholderia xenovorans LB400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF-2 like protein of unknown function (YP_553245.1) from BURKHOLDERIA XENOVORANS LB400 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: 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 1.4Feb 1, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized NTF-2 like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2305
Polymers14,8311
Non-polymers3994
Water2,324129
1
A: uncharacterized NTF-2 like protein
hetero molecules

A: uncharacterized NTF-2 like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,46110
Polymers29,6622
Non-polymers7998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6510 Å2
ΔGint-21 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.507, 60.329, 92.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein uncharacterized NTF-2 like protein


Mass: 14830.858 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans LB400 (bacteria)
Gene: YP_553245.1, Bxeno_B0927, Bxe_B2092 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13PU4

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2000M Ca(OAc)2, 40.0000% PEG-600, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97920,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97921
30.979341
ReflectionResolution: 1.85→29.185 Å / Num. obs: 15025 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.556 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 5.802
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.93.40.3732.1373310980.37399.3
1.9-1.953.40.272.8360510630.2799.2
1.95-2.013.50.2183.4354910180.21899.4
2.01-2.073.50.1824354010090.18299.6
2.07-2.143.50.1724.234219760.17299.7
2.14-2.213.50.154.833419540.1599.8
2.21-2.293.50.1375.232299150.13799.8
2.29-2.393.50.1265.631128840.12699.7
2.39-2.493.50.1126.329398430.112100
2.49-2.623.50.1016.528178100.10199.8
2.62-2.763.50.0937.327187840.09399.9
2.76-2.933.40.0897.325317360.08999.9
2.93-3.133.40.0778.223516940.07799.8
3.13-3.383.30.0649.321666490.06499.9
3.38-3.73.30.069.519556000.0699.8
3.7-4.143.20.05610.317545450.056100
4.14-4.783.20.069.415714970.06100
4.78-5.853.10.0668.212854170.066100
5.85-8.273.10.0726.610383350.072100
8.27-29.192.80.0617.85491980.06197.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.185 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.475 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (4). CA ION AND ACETATE ION (ACT) AND PEG 600 FRAGMENT (PEG AND PG4) WERE MODELED BASED ON CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 760 5.1 %RANDOM
Rwork0.185 ---
obs0.187 15003 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.57 Å2 / Biso mean: 21.351 Å2 / Biso min: 8.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 25 129 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211134
X-RAY DIFFRACTIONr_bond_other_d0.0010.02788
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9391526
X-RAY DIFFRACTIONr_angle_other_deg1.33231901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70124.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16715173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.309158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211295
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02241
X-RAY DIFFRACTIONr_mcbond_it1.6493669
X-RAY DIFFRACTIONr_mcbond_other0.5213271
X-RAY DIFFRACTIONr_mcangle_it2.56551068
X-RAY DIFFRACTIONr_scbond_it3.3595465
X-RAY DIFFRACTIONr_scangle_it5.0188458
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 64 -
Rwork0.194 1030 -
all-1094 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 7.3098 Å / Origin y: 11.0523 Å / Origin z: 18.563 Å
111213212223313233
T-0.0372 Å2-0.0188 Å20.0059 Å2--0.0707 Å20.0025 Å2---0.0315 Å2
L1.4229 °2-0.0846 °20.1567 °2-1.5327 °20.1588 °2--0.6255 °2
S-0.0007 Å °0.1281 Å °0.0575 Å °-0.0643 Å °-0.0124 Å °-0.1083 Å °-0.1 Å °0.1414 Å °0.0131 Å °

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