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- PDB-3fgy: CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (BXE_B1094) FROM BURKHOL... -

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Basic information

Entry
Database: PDB / ID: 3fgy
TitleCRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (BXE_B1094) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.59 A RESOLUTION
Componentsuncharacterized NTF2-like protein
KeywordsUNKNOWN FUNCTION / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / 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
DI(HYDROXYETHYL)ETHER / Unknown ligand / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesBurkholderia xenovorans LB400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function. (YP_554211.1) from BURKHOLDERIA XENOVORANS LB400 at 1.59 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 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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
B: uncharacterized NTF2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1796
Polymers29,9672
Non-polymers2124
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-2 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.950, 66.080, 91.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS AND STATIC LIGHT SCATTERING SUGGEST THAT THIS IS THE STABLE OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein uncharacterized NTF2-like protein


Mass: 14983.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans LB400 (bacteria)
Gene: Bxeno_B1893, Bxe_B1094, YP_554211.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13M28
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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. A C-TERMINAL FRAMESHIFT RESULTS IN SEQUENCE CHANGES FOR THE LAST THREE RESIDUES OF THE TARGET SEQUENCE (Y129T, E130N AND L131F) AND THREE ADDITIONAL RESIDUES (132N, 133A AND 134T) AT THE C-TERMINUS.

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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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 30.0000% PEG-400, 0.1M CAPS pH 10.5, 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: 0.94645,0.97967
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
20.979671
ReflectionResolution: 1.59→29.037 Å / Num. obs: 37939 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 20.169 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.59-1.650.4461.7141817542199.4
1.65-1.710.3422.2122646489199.5
1.71-1.790.2453.1138957350199.1
1.79-1.880.1674.5129846843199.3
1.88-20.1027.5138017247197.9
2-2.160.06411.5139107309198.2
2.16-2.370.07715.7155306883198.4
2.37-2.720.0920.7231497315199.6
2.72-3.420.04733.2272897150199.8
3.42-29.0370.02648.2276797206199.2

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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: 1.59→29.037 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.302 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PEG MOLECULES (PEG) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.AN UNIDENITIFIED LIGAND (UNL) HAS BEEN MODELED IN CHAIN B AT WHAT COULD BE THE PUTATIVE ACTIVE SITE BASED ON COMPARISON WITH A LIGAND BOUND IN THE LIMONENE-1,2-EPOXIDE HYDROLASE WITH PDB ACCESSION CODE 1NU3.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1890 5 %RANDOM
Rwork0.183 ---
obs0.184 37883 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.11 Å2 / Biso mean: 23.121 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 26 329 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222227
X-RAY DIFFRACTIONr_bond_other_d0.0020.021508
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9553050
X-RAY DIFFRACTIONr_angle_other_deg0.94933695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78223.71197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.2120.2426
X-RAY DIFFRACTIONr_nbd_other0.2080.21589
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21111
X-RAY DIFFRACTIONr_nbtor_other0.0880.21211
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.232
X-RAY DIFFRACTIONr_mcbond_it1.95231507
X-RAY DIFFRACTIONr_mcbond_other0.473562
X-RAY DIFFRACTIONr_mcangle_it2.6252248
X-RAY DIFFRACTIONr_scbond_it4.228926
X-RAY DIFFRACTIONr_scangle_it5.55411780
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 133 -
Rwork0.253 2609 -
all-2742 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8595-0.4471-0.24250.8489-0.35531.1947-0.0653-0.19590.02340.1690.011-0.1772-0.02670.18880.0542-0.0072-0.0085-0.03430.01370.0092-0.023740.626344.283121.5655
20.578-0.17470.02491.0138-0.18070.1358-0.0108-0.0195-0.0055-0.02550.03380.15910.028-0.0515-0.0231-0.0282-0.0134-0.0101-0.03410.0063-0.023220.521350.717111.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 134
2X-RAY DIFFRACTION2B0 - 130

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