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- PDB-3er7: Crystal structure of NTF2-like protein of unknown function (YP_00... -

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Basic information

Entry
Database: PDB / ID: 3er7
TitleCrystal structure of NTF2-like protein of unknown function (YP_001812677.1) from EXIGUOBACTERIUM SP. 255-15 at 1.50 A resolution
Componentsuncharacterized NTF2-like protein
Keywordsstructural genomics / unknown function / YP_001812677.1 / 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 / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Function and homology information
Biological speciesExiguobacterium sibiricum 255-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (YP_001812677.1) from EXIGUOBACTERIUM SP. 255-15 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 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 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)30,4335
Polymers30,1852
Non-polymers2483
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-5 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.680, 91.680, 33.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 5 - 122 / Label seq-ID: 6 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS FORMING A DIMER. CRYSTAL PACKING ANALYSIS SUGGESTS THAT THIS IS THE OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein uncharacterized NTF2-like protein


Mass: 15092.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum 255-15 (bacteria)
Gene: YP_001812677.1, Exig_0174 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B1YHC8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 305 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, 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: 0.91162,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 10, 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
20.97921
ReflectionResolution: 1.5→29.514 Å / Num. obs: 40169 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.153 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.610.4251.913589723097
1.61-1.670.3212.411954632099.6
1.67-1.750.2543.113587717599.3
1.75-1.840.1744.412510658399.2
1.84-1.950.1057.212569657499.1
1.95-2.10.06810.613056681199.1
2.1-2.310.04714.613114682098.8
2.31-2.650.03718.413458697599.2
2.65-3.330.02426.713140677699
3.330.01934.913402685998.2

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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
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.514 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.82 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078
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.CHLORIDE AND PEG (PEG3000 FRAGMENTS) FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.IT APPEARS PLAUSIBLE THAT A DISULFIDE BOND MAY FORM BETWEEN CYS87 RESIDUES IN CHAINS A AND B.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2014 5 %RANDOM
Rwork0.176 ---
obs0.178 40122 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.56 Å2 / Biso mean: 19.085 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 13 305 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222028
X-RAY DIFFRACTIONr_bond_other_d0.0050.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9282766
X-RAY DIFFRACTIONr_angle_other_deg0.99233254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5875268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32124.554101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1215336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022323
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
X-RAY DIFFRACTIONr_nbd_refined0.220.2421
X-RAY DIFFRACTIONr_nbd_other0.2040.21341
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2955
X-RAY DIFFRACTIONr_nbtor_other0.0870.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.222
X-RAY DIFFRACTIONr_mcbond_it1.6821281
X-RAY DIFFRACTIONr_mcbond_other0.312508
X-RAY DIFFRACTIONr_mcangle_it2.40242003
X-RAY DIFFRACTIONr_scbond_it3.9176874
X-RAY DIFFRACTIONr_scangle_it5.2168747
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1506 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.335
LOOSE THERMAL2.2310
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 143 -
Rwork0.271 2740 -
all-2883 -
obs--98.3 %
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)
11.08330.58190.19690.90820.54350.94530.0332-0.0364-0.08230.0367-0.0150.00050.1059-0.1029-0.0182-0.0277-0.0094-0.0085-0.02230.0006-0.033242.462116.964417.7441
21.47690.51950.16891.24570.06230.46560.0554-0.06820.2698-0.0081-0.06970.0512-0.11120.00490.0144-0.0209-0.01120.0259-0.0339-0.0248-0.002755.638541.910823.3269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 122
2X-RAY DIFFRACTION2B5 - 127

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