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- PDB-3fsd: Crystal structure of NTF2-like protein of unknown function in nut... -

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Basic information

Entry
Database: PDB / ID: 3fsd
TitleCrystal structure of NTF2-like protein of unknown function in nutrient uptake (YP_427473.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.70 A resolution
ComponentsNTF2-like protein of unknown function in nutrient uptake
Keywordsstructural genomics / unknown function / YP_427473.1 / NTF2-like protein of unknown function in nutrient uptake / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyDomain 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 / Unknown ligand / DUF4440 domain-containing protein
Function and homology information
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function in nutrient uptake (YP_427473.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 17, 2016Group: Refinement description
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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 1.6Feb 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

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Assembly

Deposited unit
A: NTF2-like protein of unknown function in nutrient uptake
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7394
Polymers14,6141
Non-polymers1243
Water1,67593
1
A: NTF2-like protein of unknown function in nutrient uptake
hetero molecules

A: NTF2-like protein of unknown function in nutrient uptake
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4778
Polymers29,2292
Non-polymers2486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4090 Å2
ΔGint-4 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.018, 61.018, 56.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-218-

HOH

21A-219-

HOH

31A-220-

HOH

41A-222-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION. THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION IS SUPPORTED BY ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING.

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Components

#1: Protein NTF2-like protein of unknown function in nutrient uptake


Mass: 14614.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: Rru_A2386, YP_427473.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2RRQ9
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 1.8 Å3/Da / Density % sol: 31.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.0% polyethylene glycol 3350, 0.2M magnesium chloride, ADDITIVE: 0.001M uridine 5'-monophosphate (UMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97867,0.97776,0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978671
20.977761
30.911621
ReflectionResolution: 1.7→27.287 Å / Num. obs: 12272 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 20.479 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.749.60.7552.484438840.755100
1.74-1.799.50.6382118600.6100
1.79-1.849.50.4534.181458540.453100
1.84-1.99.60.3735.176528010.373100
1.9-1.969.60.2846.876077940.284100
1.96-2.039.50.248.174767850.24100
2.03-2.119.50.19110.270797430.191100
2.11-2.199.50.16312.667477070.163100
2.19-2.299.50.13915.164966860.139100
2.29-2.49.50.13916.562476570.139100
2.4-2.539.40.13318.260536420.133100
2.53-2.699.30.12320.856686070.123100
2.69-2.879.30.10725.452475620.107100
2.87-3.19.30.08528.949285320.085100
3.1-3.49.30.0693445684920.069100
3.4-3.89.30.0636.542174550.06100
3.8-4.3990.0564036664060.056100
4.39-5.3890.05539.431013450.055100
5.38-7.68.40.05533.524092860.055100
7.6-27.297.40.05134.612861740.05198.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.287 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.352 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.115
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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE. 4.1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.GLY 118 IN CHAIN A HAS BEEN MODELED INTO POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 585 4.8 %RANDOM
Rwork0.172 ---
obs0.175 12236 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.65 Å2 / Biso mean: 24.583 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---1.23 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 18 93 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022966
X-RAY DIFFRACTIONr_bond_other_d0.0020.02652
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9711312
X-RAY DIFFRACTIONr_angle_other_deg0.98431574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87821.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75915158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.511511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined0.1890.201141
X-RAY DIFFRACTIONr_nbd_other0.2140.2680
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2447
X-RAY DIFFRACTIONr_nbtor_other0.090.2578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.215
X-RAY DIFFRACTIONr_mcbond_it2.5563651
X-RAY DIFFRACTIONr_mcbond_other0.6333254
X-RAY DIFFRACTIONr_mcangle_it3.5565972
X-RAY DIFFRACTIONr_scbond_it5.5138387
X-RAY DIFFRACTIONr_scangle_it7.04111338
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 35 -
Rwork0.234 849 -
all-884 -
obs--100 %

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