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- PDB-3flj: Crystal structure of uncharacterized protein conserved in bacteri... -

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Basic information

Entry
Database: PDB / ID: 3flj
TitleCrystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution
Componentsuncharacterized protein conserved in bacteria with a cystatin-like fold
Keywordsstructural genomics / unknown function / YP_168589.1 / uncharacterized protein conserved in bacteria with a cystatin-like fold / 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 / Unknown ligand / SnoaL-like domain-containing protein
Function and homology information
Biological speciesSILICIBACTER POMEROYI DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein conserved in bacteria with a cystatin-like fold


Theoretical massNumber of molelcules
Total (without water)18,1032
Polymers18,1031
Non-polymers01
Water1,892105
1
A: uncharacterized protein conserved in bacteria with a cystatin-like fold

A: uncharacterized protein conserved in bacteria with a cystatin-like fold


Theoretical massNumber of molelcules
Total (without water)36,2074
Polymers36,2072
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area3060 Å2
ΔGint-12 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.880, 120.880, 120.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein uncharacterized protein conserved in bacteria with a cystatin-like fold


Mass: 18103.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SILICIBACTER POMEROYI DSS-3 (bacteria) / Gene: SPO3393, YP_168589.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LN19
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 4.07 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M MgCl2, 2.5000M NaCl, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97982
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979821
ReflectionResolution: 2→28.49 Å / Num. obs: 19903 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.973 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.95
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.8661.4102583591196.2
2.07-2.150.6281.8106913738199.6
2.15-2.250.4492.6112653942199.5
2.25-2.370.3333.4112273915199.4
2.37-2.520.2424.6111053850199.6
2.52-2.710.1796.2109063780199.6
2.71-2.990.129.3113703920199.5
2.99-3.420.05916.8111053840199.7
3.42-4.30.02831.8110163789199.3
4.3-28.490.0241.2112143845198.7

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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: 2→28.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.615 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.098
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN THE CORE OF THE PROTEIN SURROUNDED BY BOTH HYDROPHOBIC AND HYDROPHILLIC RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1018 5.1 %RANDOM
Rwork0.176 ---
obs0.177 19902 99.87 %-
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: 90.63 Å2 / Biso mean: 48.955 Å2 / Biso min: 30.92 Å2
Refinement stepCycle: LAST / Resolution: 2→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 4 105 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221190
X-RAY DIFFRACTIONr_bond_other_d0.0050.02826
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9571618
X-RAY DIFFRACTIONr_angle_other_deg1.55531994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8585154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.32722.24158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3515207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7771513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021348
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02271
X-RAY DIFFRACTIONr_nbd_refined0.1560.2173
X-RAY DIFFRACTIONr_nbd_other0.1180.2810
X-RAY DIFFRACTIONr_nbtor_refined0.140.2548
X-RAY DIFFRACTIONr_nbtor_other0.0660.2586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0750.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0590.26
X-RAY DIFFRACTIONr_mcbond_it1.1882878
X-RAY DIFFRACTIONr_mcbond_other0.1472295
X-RAY DIFFRACTIONr_mcangle_it1.6841158
X-RAY DIFFRACTIONr_scbond_it3.3696533
X-RAY DIFFRACTIONr_scangle_it4.5018453
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 71 -
Rwork0.255 1405 -
all-1476 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 58.497 Å / Origin y: 24.106 Å / Origin z: 11.656 Å
111213212223313233
T-0.0654 Å2-0.0052 Å20.0481 Å2--0.1702 Å2-0.0241 Å2---0.1393 Å2
L1.4638 °20.698 °2-0.5356 °2-1.8298 °2-1.0984 °2--1.8462 °2
S0.0112 Å °-0.1935 Å °0.1196 Å °0.1655 Å °-0.083 Å °0.0157 Å °0.1434 Å °0.0594 Å °0.0718 Å °

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