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- PDB-4r1k: Crystal structure of a NTF2-like protein (EUBSIR_01394) from Euba... -

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Basic information

Entry
Database: PDB / ID: 4r1k
TitleCrystal structure of a NTF2-like protein (EUBSIR_01394) from Eubacterium siraeum DSM 15702 at 2.56 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NTF2-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF5104 / Domain of unknown function (DUF5104) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / DUF5104 domain-containing protein
Function and homology information
Biological speciesEubacterium siraeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.56 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (EUBSIR_01394) from Eubacterium siraeum DSM 15702 at 2.56 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,8512
Polymers32,8512
Non-polymers00
Water724
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,4251
Polymers16,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,4251
Polymers16,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.646, 59.318, 58.411
Angle α, β, γ (deg.)90.000, 101.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein


Mass: 16425.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium siraeum (bacteria) / Strain: DSM 15702 / Gene: EUBSIR_01394 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B0MNI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 30-166 OF 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M magnesium acetate, 30.0% 2-methyl-2,4-pentanediol, 0.1M sodium cacodylate pH 6.5, 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: 0.97939,0.91837,0.97882
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.918371
30.978821
ReflectionResolution: 2.56→42.844 Å / Num. obs: 11309 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.294 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.56-2.650.6522.14245110997.5
2.65-2.760.5442.54217115397.8
2.76-2.880.3523.63713104795.7
2.88-3.030.245.44488112899
3.03-3.220.1587.64513114299.3
3.22-3.470.11510.24444114298.3
3.47-3.820.0912.64263114598.7
3.82-4.370.0616.83857108794.4
4.37-5.480.05319.84446114398.6
5.480.05120.44287117296.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.56→42.844 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 29.488 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.357
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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
Rfree0.2989 543 4.8 %RANDOM
Rwork0.2528 ---
obs0.2551 10762 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 96.34 Å2 / Biso mean: 48.3173 Å2 / Biso min: 30.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å2-0 Å24.95 Å2
2---5.55 Å2-0 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.56→42.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 0 4 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192285
X-RAY DIFFRACTIONr_bond_other_d0.0040.021990
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9423074
X-RAY DIFFRACTIONr_angle_other_deg1.08434610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.45525.63135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54815373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.965156
X-RAY DIFFRACTIONr_chiral_restr0.080.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022665
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02557
X-RAY DIFFRACTIONr_mcbond_it1.6642.5531082
X-RAY DIFFRACTIONr_mcbond_other1.6562.551081
X-RAY DIFFRACTIONr_mcangle_it2.6544.7731349
LS refinement shellResolution: 2.56→2.626 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 27 -
Rwork0.358 793 -
all-820 -
obs--98.68 %
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)
12.70260.4183-0.68591.3986-0.47180.9596-0.13950.1557-0.0083-0.34590.10140.06180.1719-0.01090.03820.4134-0.0121-0.10950.4871-0.00920.177913.02236.28751.19
22.6383-0.8736-0.83922.38950.07362.4496-0.04480.1844-0.0302-0.08910.09590.01610.0022-0.0888-0.0510.2828-0.0233-0.10760.5735-0.02610.139236.4947.44736.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 163
2X-RAY DIFFRACTION2B0 - 164

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