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- PDB-3f14: Crystal structure of NTF2-like protein of unknown function (YP_68... -

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Basic information

Entry
Database: PDB / ID: 3f14
TitleCrystal structure of NTF2-like protein of unknown function (YP_680363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.45 A resolution
Componentsuncharacterized NTF2-like protein
Keywordsstructural genomics / unknown function / YP_680363.1 / NTF2-like protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-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 / TRIETHYLENE GLYCOL / SnoaL-like domain-containing protein
Function and homology information
Biological speciesCytophaga hutchinsonii ATCC 33406 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (YP_680363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized NTF2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1473
Polymers12,8751
Non-polymers2722
Water1,910106
1
A: uncharacterized NTF2-like protein
hetero molecules

A: uncharacterized NTF2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2956
Polymers25,7502
Non-polymers5454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area2990 Å2
ΔGint3 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.640, 57.640, 59.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein uncharacterized NTF2-like protein


Mass: 12875.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria)
Gene: CHU_3788, YP_680363.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11NJ3
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, 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: 0.91162,0.97939,0.97925
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
20.979391
30.979251
ReflectionResolution: 1.45→25.933 Å / Num. obs: 20633 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.16 % / Biso Wilson estimate: 17.008 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.58
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.45-1.50.5382.5135493671198.8
1.5-1.560.3773.6148593965199.8
1.56-1.630.2665144503839199.8
1.63-1.720.1876.9155354101199.8
1.72-1.830.1329.6150783971199.9
1.83-1.970.08214.5148583907199.9
1.97-2.170.05421.7148533892199.8
2.17-2.480.04126.6147443850199.7
2.48-3.120.03233.5148873872199.6
3.12-25.9330.02541.8149833931199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→25.933 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.333 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.064
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 ...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 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. 4.PEG MOLECULE AND TRIS ANION FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1054 5.1 %RANDOM
Rwork0.171 ---
obs0.171 20606 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.03 Å2 / Biso mean: 20.996 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 18 106 997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221039
X-RAY DIFFRACTIONr_bond_other_d0.0020.02672
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9351417
X-RAY DIFFRACTIONr_angle_other_deg1.03331653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.66225.96252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5315166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.342151
X-RAY DIFFRACTIONr_chiral_restr0.0880.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021204
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02216
X-RAY DIFFRACTIONr_nbd_refined0.2850.3202
X-RAY DIFFRACTIONr_nbd_other0.1820.3696
X-RAY DIFFRACTIONr_nbtor_refined0.1840.5519
X-RAY DIFFRACTIONr_nbtor_other0.0880.5518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5168
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0650.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.526
X-RAY DIFFRACTIONr_mcbond_it2.1483700
X-RAY DIFFRACTIONr_mcbond_other0.5033252
X-RAY DIFFRACTIONr_mcangle_it2.6951037
X-RAY DIFFRACTIONr_scbond_it5.3698450
X-RAY DIFFRACTIONr_scangle_it6.44211380
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 81 -
Rwork0.208 1398 -
all-1479 -
obs--99.13 %
Refinement TLS params.Method: refined / Origin x: 45.6928 Å / Origin y: 18.9197 Å / Origin z: 7.735 Å
111213212223313233
T-0.015 Å2-0.008 Å20.0204 Å2--0.0476 Å2-0.0179 Å2---0.0227 Å2
L1.4244 °21.2321 °20.6811 °2-1.8289 °20.5826 °2--2.1145 °2
S-0.0721 Å °0.1481 Å °-0.1538 Å °-0.1999 Å °0.1425 Å °-0.127 Å °0.0979 Å °0.0914 Å °-0.0703 Å °

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