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- PDB-3grd: Crystal structure of NTF2-superfamily protein with unknown functi... -

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Basic information

Entry
Database: PDB / ID: 3grd
TitleCrystal structure of NTF2-superfamily protein with unknown function (NP_977240.1) from BACILLUS CEREUS ATCC 10987 at 1.25 A resolution
Componentsuncharacterized NTF2-superfamily protein
Keywordsstructural genomics / unknown function / NP_977240.1 / NTF2-superfamily protein with 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 / ACETATE ION / SnoaL-like domain-containing protein
Function and homology information
Biological speciesBacillus cereus ATCC 10987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-superfamily protein with unknown function (NP_977240.1) from BACILLUS CEREUS ATCC 10987 at 1.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / 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-superfamily protein
B: uncharacterized NTF2-superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7216
Polymers30,5572
Non-polymers1644
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-28 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.090, 47.140, 151.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein uncharacterized NTF2-superfamily protein


Mass: 15278.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 10987 (bacteria) / Gene: BCE_0917, NP_977240.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q73CZ7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.29
Details: 33.8000% polyethylene glycol 4000, 0.2000M sodium acetate, 0.1M TRIS pH 8.29, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97862
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 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
10.911621
20.978621
ReflectionResolution: 1.25→29.566 Å / Num. obs: 81747 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.01 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.63
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.25-1.290.4691.6202161167182.5
1.29-1.350.3872308461742895.2
1.35-1.410.3012.6264471471996
1.41-1.480.2293.4260041431396.4
1.48-1.570.1515.1275991500597.1
1.57-1.70.117.1307941653998.1
1.7-1.870.06810.8291171542398.7
1.87-2.140.03718.2295461546998.8
2.14-2.690.02625.3297151542698.8
2.69-29.5660.01737.8302841557998.2

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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: 1.25→29.566 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.289 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041
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. ACETATE (ACT) AND SODIUM (NA) IONS FROM CRYSTALLIZATION CONDITION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 4091 5 %RANDOM
Rwork0.133 ---
obs0.135 81659 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.76 Å2 / Biso mean: 13.625 Å2 / Biso min: 4.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 18 540 2908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212440
X-RAY DIFFRACTIONr_bond_other_d0.0010.021608
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9363328
X-RAY DIFFRACTIONr_angle_other_deg0.89333955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.72225.304115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09515429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.478157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02511
X-RAY DIFFRACTIONr_nbd_refined0.2670.2478
X-RAY DIFFRACTIONr_nbd_other0.1910.21726
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21166
X-RAY DIFFRACTIONr_nbtor_other0.0880.21293
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2389
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.251
X-RAY DIFFRACTIONr_mcbond_it2.36231514
X-RAY DIFFRACTIONr_mcbond_other1.6483615
X-RAY DIFFRACTIONr_mcangle_it3.16452450
X-RAY DIFFRACTIONr_scbond_it4.5438965
X-RAY DIFFRACTIONr_scangle_it6.06611878
X-RAY DIFFRACTIONr_rigid_bond_restr1.99134257
X-RAY DIFFRACTIONr_sphericity_free9.0933542
X-RAY DIFFRACTIONr_sphericity_bonded4.43633974
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 274 -
Rwork0.23 5289 -
all-5563 -
obs--92.29 %

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