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- PDB-3dmc: CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (AVA_2261) FROM ANABAENA... -

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Basic information

Entry
Database: PDB / ID: 3dmc
TitleCRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (AVA_2261) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.65 A RESOLUTION
ComponentsNTF2-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 speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a NTF2-like Protein (YP_322774.1) from ANABAENA VARIABILIS ATCC 29413 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 13, 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: NTF2-like Protein
B: NTF2-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4584
Polymers31,3402
Non-polymers1182
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-12 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.777, 42.138, 46.342
Angle α, β, γ (deg.)87.970, 65.830, 83.740
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NTF2-like Protein


Mass: 15669.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Gene: YP_322774.1, Ava_2261 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3MAV7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.69
Details: 0.17M di-ammonium hydrogen phosphate, 0.1M sodium acetate pH 4.69, 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→29.907 Å / Num. obs: 28896 / % possible obs: 92.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.693.90.4121.9583015010.41265.8
1.69-1.743.90.3312.3729318710.33183.5
1.74-1.793.90.2912.6819620870.29194.4
1.79-1.843.90.2223.4798520280.22295.2
1.84-1.913.90.1764.2756219240.17694.5
1.91-1.973.90.1495740918840.14995.3
1.97-2.053.90.1225.4717718270.12295.5
2.05-2.133.90.1046.7699717860.10495.5
2.13-2.223.90.0897.5672417120.08995.3
2.22-2.333.80.0947.1607315950.09494.8
2.33-2.463.90.0847.7605415490.08496.5
2.46-2.613.90.0758.9566114490.07596.4
2.61-2.793.90.0698.7544913980.06996.5
2.79-3.013.90.069.5501712880.0697.3
3.01-3.33.90.05410.5471912100.05497
3.3-3.693.90.04911.4409110520.04996.3
3.69-4.263.90.04612.237479700.04697.5
4.26-5.223.90.0441430948020.04497.9
5.22-7.383.80.04912.423536210.04997.8
7.38-29.913.60.05310.512353420.05397.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→29.907 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.12 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.118
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) IONS FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 4. UNEXPLAINED ELECTRON DENSITIES ON THE VAL 108 IN CHAINS A AND B WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1463 5.1 %RANDOM
Rwork0.175 ---
obs0.177 28896 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.27 Å20.18 Å2
2--0.72 Å20.35 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 8 373 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222274
X-RAY DIFFRACTIONr_bond_other_d0.0010.021549
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9183063
X-RAY DIFFRACTIONr_angle_other_deg1.39833723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55323.607122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5261512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02552
X-RAY DIFFRACTIONr_mcbond_it1.70931342
X-RAY DIFFRACTIONr_mcbond_other0.4173562
X-RAY DIFFRACTIONr_mcangle_it2.67862152
X-RAY DIFFRACTIONr_scbond_it4.5318932
X-RAY DIFFRACTIONr_scangle_it6.31411911
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 81 -
Rwork0.253 1420 -
all-1501 -
obs--65.83 %

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