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- PDB-3ec9: CRYSTAL STRUCTURE OF A NTF2-like protein (BTH_I0051) FROM BURKHOL... -

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Basic information

Entry
Database: PDB / ID: 3ec9
TitleCRYSTAL STRUCTURE OF A NTF2-like protein (BTH_I0051) FROM BURKHOLDERIA THAILANDENSIS E264 AT 1.60 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 / 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 / ACETATE ION / SnoaL-like domain-containing protein
Function and homology information
Biological speciesBurkholderia thailandensis E264 (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 (YP_440611.1) from Burkholderia thailandensis E264 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 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 1.5Nov 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

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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)32,6858
Polymers32,2982
Non-polymers3876
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-25 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.849, 52.021, 111.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein uncharacterized NTF2-like protein


Mass: 16149.042 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Gene: YP_440611.1, BTH_I0051 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2T2I4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, 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: 0.91162,0.97932,0.97920
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
20.979321
30.97921
ReflectionResolution: 1.6→27.875 Å / Num. obs: 40560 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.705 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.825
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.643.60.4981.51079329580.49899.7
1.64-1.693.70.4291.71048928730.42999.8
1.69-1.743.60.3462.21027728180.34699.9
1.74-1.793.60.2842.61001627460.284100
1.79-1.853.70.2373.1958526040.237100
1.85-1.913.70.2033.7940725660.203100
1.91-1.983.70.1684.4910224890.168100
1.98-2.073.70.1325.6876023830.132100
2.07-2.163.60.1136.5844323150.113100
2.16-2.263.70.1047802421820.104100
2.26-2.393.70.0967.5762620880.096100
2.39-2.533.70.0878724919850.087100
2.53-2.73.70.0868686418790.086100
2.7-2.923.60.0749.1640117660.074100
2.92-3.23.60.06310.2581016130.063100
3.2-3.583.60.05310.6530114690.05399.8
3.58-4.133.60.05211.4468613160.05299.6
4.13-5.063.50.0579.7390211120.05799.5
5.06-7.163.40.0659.129938830.06598.9
7.16-27.883.10.05310.516035150.05396.4

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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: 1.6→27.875 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.874 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084
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). ACETATE (ACT) IONS FROM THE CRYSTALLIZATION SOLUTION AND A GLYCEROL (GOL) MOLECULE FROM CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2031 5 %RANDOM
Rwork0.168 ---
obs0.169 40506 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.81 Å2 / Biso mean: 16.976 Å2 / Biso min: 5.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.44 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 26 359 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212278
X-RAY DIFFRACTIONr_bond_other_d0.0020.021513
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9273105
X-RAY DIFFRACTIONr_angle_other_deg0.93433636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.50422.544114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29315349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3281522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_nbd_refined0.2080.2426
X-RAY DIFFRACTIONr_nbd_other0.2010.21651
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21071
X-RAY DIFFRACTIONr_nbtor_other0.0860.21178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3590.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.213
X-RAY DIFFRACTIONr_mcbond_it1.90731461
X-RAY DIFFRACTIONr_mcbond_other0.5183562
X-RAY DIFFRACTIONr_mcangle_it2.54352253
X-RAY DIFFRACTIONr_scbond_it4.1728971
X-RAY DIFFRACTIONr_scangle_it5.99511852
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 141 -
Rwork0.216 2812 -
all-2953 -
obs--99.6 %
Refinement TLS params.

S12: -0.0093 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (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)
10.36820.19820.05160.21210.04410.45260.0180.01160.0090.02220.0612-0.012-0.038-0.0402-0.00770.01220.0011-0.01040.003-0.007215.449343.815216.668
20.2940.20980.01710.41750.03910.58780.01190.02650.00180.0158-0.05740.00930.0561-0.0277-0.01260.01250.0036-0.0111-0.0068-0.007838.020351.496218.1544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 13911 - 140
2X-RAY DIFFRACTION2BB9 - 13910 - 140

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