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- PDB-3fh1: Crystal structure of a ntf2-like protein of unknown function (mll... -

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Basic information

Entry
Database: PDB / ID: 3fh1
TitleCrystal structure of a ntf2-like protein of unknown function (mll8193) from mesorhizobium loti at 1.60 A resolution
Componentsuncharacterized NTF2-like protein
KeywordsUNKNOWN FUNCTION / Structural genomics / 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 / Unknown ligand / Mll8193 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (NP_108339.1) from MESORHIZOBIUM LOTI at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 1.5Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized NTF2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8044
Polymers14,7071
Non-polymers983
Water2,000111
1
A: uncharacterized NTF2-like protein
hetero molecules

A: uncharacterized NTF2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6098
Polymers29,4142
Non-polymers1956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4020 Å2
ΔGint-22 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.110, 45.110, 136.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein uncharacterized NTF2-like protein


Mass: 14706.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mll8193, NP_108339.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q983T0
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2000M (NH4)2HCitrate, 20.0000% PEG-3350, No Buffer pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97965
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979651
ReflectionResolution: 1.6→28.904 Å / Num. obs: 19510 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.94 % / Biso Wilson estimate: 20.689 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.65
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.661.0361.45136833655198
1.66-1.720.7711.92120333187199.3
1.72-1.80.5462.7138523656199.6
1.8-1.90.3244.4141163715199.8
1.9-2.020.1987135823566199.9
2.02-2.170.12510.6129663391199.9
2.17-2.390.08814.41387936211100
2.39-2.730.06419.11348635021100
2.73-3.440.03530.7138203584199.9
3.44-28.9040.02343.5139633605199.6

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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: 1.6→28.904 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.281 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083
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. A CHLORIDE ION, FROM THE PROTEIN BUFFER, AND AN ETHYLENE GLYCOL MOLECULE, FROM THE CRYOPROTECTANT, WERE MODELED IN THE STRUCTURE. 5.ONE UNKNOWN LIGAND IS MODELED NEAR TO RESIDUE 69 AND 96.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 990 5.1 %RANDOM
Rwork0.167 ---
obs0.169 19433 99.7 %-
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: 63.81 Å2 / Biso mean: 27.375 Å2 / Biso min: 15.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 11 111 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221101
X-RAY DIFFRACTIONr_bond_other_d0.0020.02755
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9371511
X-RAY DIFFRACTIONr_angle_other_deg0.93631819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55322.75958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2451515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021324
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02248
X-RAY DIFFRACTIONr_nbd_refined0.2270.3207
X-RAY DIFFRACTIONr_nbd_other0.2220.3815
X-RAY DIFFRACTIONr_nbtor_refined0.1770.5536
X-RAY DIFFRACTIONr_nbtor_other0.0880.5639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.5178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.380.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.534
X-RAY DIFFRACTIONr_mcbond_it2.3343829
X-RAY DIFFRACTIONr_mcbond_other0.5273272
X-RAY DIFFRACTIONr_mcangle_it2.74251115
X-RAY DIFFRACTIONr_scbond_it4.4438460
X-RAY DIFFRACTIONr_scangle_it6.39211396
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 69 -
Rwork0.236 1285 -
all-1354 -
obs--97.97 %
Refinement TLS params.Method: refined / Origin x: 17.7558 Å / Origin y: 7.946 Å / Origin z: 59.3469 Å
111213212223313233
T-0.0303 Å20.0188 Å20.0196 Å2--0.0373 Å20.0047 Å2---0.0211 Å2
L0.4468 °20.1727 °20.0952 °2-1.0947 °20.5327 °2--1.7863 °2
S-0.0031 Å °0.0348 Å °-0.0376 Å °-0.1098 Å °-0.0168 Å °-0.1118 Å °0.0992 Å °0.1256 Å °0.0199 Å °

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