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- PDB-3lyg: Crystal structure of NTF2-like protein of unknown function (YP_27... -

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Basic information

Entry
Database: PDB / ID: 3lyg
TitleCrystal structure of NTF2-like protein of unknown function (YP_270605.1) from Colwellia psychrerythraea 34H at 1.61 A resolution
ComponentsNTF2-like protein of unknown function
KeywordsStructural Genomics / Unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


SnoaL-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
Similarity search - Domain/homology
IMIDAZOLE / Unknown ligand / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.61 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (YP_270605.1) from Colwellia psychrerythraea 34H at 1.61 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1195
Polymers13,8621
Non-polymers2574
Water2,702150
1
A: NTF2-like protein of unknown function
hetero molecules

A: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,23910
Polymers27,7242
Non-polymers5148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3740 Å2
ΔGint-15 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.387, 57.387, 67.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NTF2-like protein of unknown function


Mass: 13862.056 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_3947 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47X65

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Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3.2000M (NH4)2SO4, 0.1M Bicine pH 9.0, 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: 0.91837,0.97925,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / 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
10.918371
20.979251
30.979011
ReflectionResolution: 1.61→67.335 Å / Num. obs: 15075 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.57 Å2 / Rsym value: 0.095

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.61→67.335 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.292 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.086
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. AN IMIDAZOLE WAS MODELED IN THE ACTIVE SITE. A BENZOIC ACID LIKE MOLECULE WAS MODELED AS UNL. SULFATE (SO4) AND GLYCEROL (GOL) MODELEED WERE WERE PRESENT IN CRYTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 758 5 %RANDOM
Rwork0.151 ---
obs0.152 15033 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.62 Å2 / Biso mean: 15.581 Å2 / Biso min: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.61→67.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 25 150 1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221065
X-RAY DIFFRACTIONr_bond_other_d0.0020.02733
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9781444
X-RAY DIFFRACTIONr_angle_other_deg0.91431793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43325.55654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48415193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.638155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02217
X-RAY DIFFRACTIONr_mcbond_it1.7263619
X-RAY DIFFRACTIONr_mcbond_other0.4973255
X-RAY DIFFRACTIONr_mcangle_it2.54551002
X-RAY DIFFRACTIONr_scbond_it4.0078446
X-RAY DIFFRACTIONr_scangle_it5.89611434
LS refinement shellResolution: 1.614→1.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 56 -
Rwork0.234 1033 -
all-1089 -
obs--99.73 %
Refinement TLS params.Method: refined / Origin x: 13.3645 Å / Origin y: 14.6032 Å / Origin z: 22.1808 Å
111213212223313233
T0.0188 Å2-0.002 Å2-0.0007 Å2-0.0006 Å2-0.0013 Å2--0.0103 Å2
L0.633 °2-0.1045 °20.1446 °2-0.2736 °20.0454 °2--0.5315 °2
S0.0071 Å °-0.001 Å °-0.0237 Å °-0.0482 Å °0.0057 Å °0.0019 Å °-0.0075 Å °-0.0063 Å °-0.0128 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 119
2X-RAY DIFFRACTION1A120

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