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- PDB-2rfr: Crystal structure of an ntf2-like protein with a cystatin-like fo... -

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Basic information

Entry
Database: PDB / ID: 2rfr
TitleCrystal structure of an ntf2-like protein with a cystatin-like fold (saro_3722) from novosphingobium aromaticivorans dsm at 1.16 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / 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 / SnoaL-like domain-containing protein
Function and homology information
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.16 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_001166107.1) from Novosphingobium aromaticivorans DSM 12444 at 1.16 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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: pdbx_struct_special_symmetry / 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 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,8881
Polymers16,8881
Non-polymers00
Water4,864270
1
A: Uncharacterized protein

A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)50,6633
Polymers50,6633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.135, 63.135, 75.118
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-174-

HOH

21A-218-

HOH

31A-219-

HOH

41A-225-

HOH

51A-421-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 16887.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_001166107.1, Saro_3722 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4XF70
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 20.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9797, 1.0000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
211
ReflectionResolution: 1.16→27.338 Å / Num. obs: 60052 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.28 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.16-1.193.10.6181.21279041700.61894.4
1.19-1.223.80.61.31619142490.699.1
1.22-1.264.30.5581.41821442070.55899.9
1.26-1.34.70.4851.61879840400.485100
1.3-1.344.80.4161.81918739720.416100
1.34-1.394.90.3522.11880638050.35299.9
1.39-1.4450.3022.51856536970.30299.9
1.44-1.55.10.2353.11806435480.235100
1.5-1.565.10.1913.81742634050.19199.8
1.56-1.645.10.1554.61670632640.155100
1.64-1.735.10.13651598731240.136100
1.73-1.835.10.1245.41505129590.124100
1.83-1.965.10.1135.61423927850.113100
1.96-2.1250.1055.61295025990.105100
2.12-2.324.90.1055.61162223940.10599.7
2.32-2.594.60.0856.91003621800.085100
2.59-35.30.05311.71015919270.05399.3
3-3.675.40.04214.7889516530.042100
3.67-5.195.30.03716.6694113110.037100
5.19-27.3384.90.03815.937267630.03899.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.16→27.338 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.039 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033
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.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2995 5 %RANDOM
Rwork0.141 ---
obs0.142 60050 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.16→27.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 270 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211310
X-RAY DIFFRACTIONr_bond_other_d0.0020.02885
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9361794
X-RAY DIFFRACTIONr_angle_other_deg1.01732128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72721.77462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0991518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02310
X-RAY DIFFRACTIONr_nbd_refined0.2760.2257
X-RAY DIFFRACTIONr_nbd_other0.2250.21015
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2641
X-RAY DIFFRACTIONr_nbtor_other0.0880.2814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3440.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.234
X-RAY DIFFRACTIONr_mcbond_it2.843977
X-RAY DIFFRACTIONr_mcbond_other1.8123346
X-RAY DIFFRACTIONr_mcangle_it3.16451345
X-RAY DIFFRACTIONr_scbond_it5.2098512
X-RAY DIFFRACTIONr_scangle_it6.92211449
X-RAY DIFFRACTIONr_rigid_bond_restr2.21732568
X-RAY DIFFRACTIONr_sphericity_free11.7493272
X-RAY DIFFRACTIONr_sphericity_bonded5.33332162
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 203 -
Rwork0.273 3956 -
all-4159 -
obs--94.07 %

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