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- PDB-4q53: Crystal structure of a DUF4783 family protein (BACUNI_04292) from... -

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Basic information

Entry
Database: PDB / ID: 4q53
TitleCrystal structure of a DUF4783 family protein (BACUNI_04292) from Bacteroides uniformis ATCC 8492 at 1.27 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystatin-like fold / DUF4783 / PF16022 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Protein of unknown function DUF4783 / Domain of unknown function (DUF4783) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / IODIDE ION / TRIETHYLENE GLYCOL / DUF4783 domain-containing protein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.27 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_04292) from Bacteroides uniformis ATCC 8492 at 1.27 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,34326
Polymers24,9172
Non-polymers2,42524
Water3,315184
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,59713
Polymers12,4591
Non-polymers1,13912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,74513
Polymers12,4591
Non-polymers1,28712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.136, 37.109, 61.376
Angle α, β, γ (deg.)90.00, 121.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-212-

NA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 12458.679 Da / Num. of mol.: 2 / Fragment: UNP residues 22-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_04292 / Plasmid: SpeedE5T / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V9L7

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Non-polymers , 8 types, 208 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 21-130) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-130) 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.07M Sodium Iodide, 30.00% polyethylene glycol 3350, 0.01M ferric(III) chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL11-110.97882
2
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2013
Details: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97882 Å / Relative weight: 1
ReflectionResolution: 1.27→28.002 Å / Num. obs: 53919 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.53 Å2
Reflection shellResolution: 1.27→1.32 Å / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
PHENIX1.8.4refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.27→28 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.09 / Phase error: 14.2 / Stereochemistry target values: MLHL
Details: 1. 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 ...Details: 1. 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. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. IODIDES (IOD) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. THE MODELING OF IODIDE IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS. 4. POLYETHYLENE GLYCOL FRAGMENTS (7PE,PEG, AND PG4) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 5. SODIUM (NA) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 1,2- ETHANEDIOL (EDO), USED AS A CRYOPROTECTANT, HAS ALSO BEEN MODELED INTO THE STRUCTURE. 5. HYDROGENS HAVE BEEN ADDED AT THE RIDING POSITIONS. 6. ELECTRON DENSITY INDICATES THAT CYS 109 ON THE TWO SUBUNITS IN THE ASYMMETRIC UNIT ARE OXIDIZED; THEREFORE, THESE RESIDUES WERE MODELED AS S-HYDROXYCYSTEINE (CSO).
RfactorNum. reflection% reflection
Rfree0.176 2753 5.11 %
Rwork0.154 --
obs0.155 53907 98.1 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.42 Å2
Refinement stepCycle: LAST / Resolution: 1.27→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 82 184 1970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112084
X-RAY DIFFRACTIONf_angle_d1.7252813
X-RAY DIFFRACTIONf_dihedral_angle_d18.421865
X-RAY DIFFRACTIONf_chiral_restr0.079293
X-RAY DIFFRACTIONf_plane_restr0.01372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.29190.19661450.15472514X-RAY DIFFRACTION98
1.2919-1.31540.20371310.14162578X-RAY DIFFRACTION99
1.3154-1.34070.18391310.13292506X-RAY DIFFRACTION98
1.3407-1.36810.16331490.12762558X-RAY DIFFRACTION98
1.3681-1.39780.15281310.12142560X-RAY DIFFRACTION99
1.3978-1.43030.18211190.11472585X-RAY DIFFRACTION98
1.4303-1.46610.18031290.11422587X-RAY DIFFRACTION99
1.4661-1.50570.14721510.10392552X-RAY DIFFRACTION99
1.5057-1.550.12951240.1022543X-RAY DIFFRACTION98
1.55-1.60.14831380.10492515X-RAY DIFFRACTION98
1.6-1.65720.15281490.11022579X-RAY DIFFRACTION99
1.6572-1.72360.15281410.1152574X-RAY DIFFRACTION99
1.7236-1.8020.18091650.12362571X-RAY DIFFRACTION99
1.802-1.8970.151540.12762542X-RAY DIFFRACTION99
1.897-2.01580.17591300.12782487X-RAY DIFFRACTION96
2.0158-2.17140.16361290.13482622X-RAY DIFFRACTION99
2.1714-2.38980.16851640.14782556X-RAY DIFFRACTION99
2.3898-2.73530.18671210.16162552X-RAY DIFFRACTION96
2.7353-3.4450.19521310.17682534X-RAY DIFFRACTION96
3.445-26.90790.18831210.20332639X-RAY DIFFRACTION96

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