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- PDB-3oao: Crystal structure of a protein with unknown function from DUF2059... -

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Basic information

Entry
Database: PDB / ID: 3oao
TitleCrystal structure of a protein with unknown function from DUF2059 family (PA0856) from PSEUDOMONAS AERUGINOSA at 2.72 A resolution
Componentsuncharacterized protein from DUF2059 family
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF2059 / Uncharacterized protein conserved in bacteria (DUF2059) / PHOSPHATE ION / DUF2059 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a protein with unknown function from DUF2059 family (PA0856) from PSEUDOMONAS AERUGINOSA at 2.72 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein from DUF2059 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8615
Polymers16,5401
Non-polymers3204
Water0
1
A: uncharacterized protein from DUF2059 family
hetero molecules

A: uncharacterized protein from DUF2059 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72210
Polymers33,0812
Non-polymers6418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7250 Å2
ΔGint-119 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.582, 72.582, 81.498
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein uncharacterized protein from DUF2059 family


Mass: 16540.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0856 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9I585
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Sequence detailsTHE CONSTRUCT (RESIDUES 37-182) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 37-182) 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: 3.75 Å3/Da / Density % sol: 67.17 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND SIGMA(I)>.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 65.0% MPD, 0.1M TRIS pH 8.0, 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: 0.97939,0.91837,0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2010 / 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
10.979391
20.918371
30.978951
ReflectionResolution: 2.72→29.324 Å / Num. obs: 6928 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 100.287 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.72-2.820.9431.33496122491.3
2.82-2.930.5482.23657125999.6
2.93-3.060.3753.13650125699.7
3.06-3.220.2185.13748129099.8
3.22-3.420.09111.23818131199.7
3.42-3.690.05218.63800130699.4
3.69-4.060.03128.53853132399.8
4.06-4.640.02437.33623125199.7
4.64-5.820.01943.43747130099.7
5.820.01848.73432123292.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.72→29.324 Å / Cor.coef. Fo:Fc: 0.9513 / Cor.coef. Fo:Fc free: 0.9377 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
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. PHOSPHATE (PO4) FROM PROTEIN BUFFER ARE MODELED. 3. RAMACHANDRAN OUTLIER A74 IS LOCATED IN A REGION WITH POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 324 4.69 %RANDOM
Rwork0.2087 ---
obs0.2101 6905 --
Displacement parametersBiso max: 224.76 Å2 / Biso mean: 121.9284 Å2 / Biso min: 83.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.386 Å20 Å20 Å2
2--2.386 Å20 Å2
3----4.772 Å2
Refinement stepCycle: LAST / Resolution: 2.72→29.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 16 0 1091
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d392SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes153HARMONIC5
X-RAY DIFFRACTIONt_it1103HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion144SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1247SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1103HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1490HARMONIC30.88
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion19.8
LS refinement shellResolution: 2.72→3.04 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2827 102 5.32 %
Rwork0.2303 1815 -
all0.233 1917 -
Refinement TLS params.Method: refined / Origin x: 51.3497 Å / Origin y: 7.3023 Å / Origin z: 13.0126 Å
111213212223313233
T0.0547 Å2-0.0881 Å2-0.0837 Å2--0.3885 Å20.074 Å2---0.2381 Å2
L0.2682 °20.4937 °2-0.1898 °2-1.9021 °2-1.4431 °2--0.8711 °2
S-0.4632 Å °0.1435 Å °0.0626 Å °0.1242 Å °0.0763 Å °-0.2406 Å °-0.2742 Å °0.4889 Å °0.3869 Å °
Refinement TLS groupSelection details: { A|* }

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