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- PDB-4f98: Crystal structure of a DUF2790 family protein (PA3229) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 4f98
TitleCrystal structure of a DUF2790 family protein (PA3229) from Pseudomonas aeruginosa PAO1 at 1.26 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF10976 family protein / DUF2790 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF2790 / Protein of unknown function DUF2790 / Protein of unknown function (DUF2790) / Spermidine Synthase; Chain: A, domain 2 / Roll / Mainly Beta / DUF2790 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.26 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PA3229) from Pseudomonas aeruginosa PAO1 at 1.26 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 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 ...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 1.5Nov 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: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8442
Polymers7,7521
Non-polymers921
Water1,20767
1
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6894
Polymers15,5052
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area2510 Å2
ΔGint-15 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.541, 58.728, 24.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hypothetical protein


Mass: 7752.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3229 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9HZ11
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 21-88) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 21-88) 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: 1.8 Å3/Da / Density % sol: 31.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.0% Glycerol 24.0% polyethylene glycol 1500, 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: 0.91837,0.97906,0.97884
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 2, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979061
30.978841
ReflectionResolution: 1.26→38.541 Å / Num. obs: 15636 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.005 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.26-1.310.73726500169399.7
1.31-1.360.5742.65645145699.9
1.36-1.420.4233.45726147999.6
1.42-1.490.3284.55638145199.8
1.49-1.590.2056.96458165399.5
1.59-1.710.1399.55850150699.9
1.71-1.880.08914.26108156299.7
1.88-2.150.04722.85991155999
2.15-2.710.03529.56081161399.2
2.710.02538.25818166496.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.26→38.541 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.684 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.044
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.
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 779 5 %RANDOM
Rwork0.1436 ---
obs0.145 15593 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.55 Å2 / Biso mean: 15.8642 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.26→38.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 6 67 555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021562
X-RAY DIFFRACTIONr_bond_other_d0.0030.02385
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.954776
X-RAY DIFFRACTIONr_angle_other_deg1.1923944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.866579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.87323.33327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.0291595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.799154
X-RAY DIFFRACTIONr_chiral_restr0.0910.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021645
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02118
X-RAY DIFFRACTIONr_mcbond_it2.3553334
X-RAY DIFFRACTIONr_mcbond_other0.9883137
X-RAY DIFFRACTIONr_mcangle_it3.4485552
X-RAY DIFFRACTIONr_scbond_it4.0558228
X-RAY DIFFRACTIONr_scangle_it5.40311214
X-RAY DIFFRACTIONr_rigid_bond_restr1.4873947
X-RAY DIFFRACTIONr_sphericity_free10.19567
X-RAY DIFFRACTIONr_sphericity_bonded4.1295925
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 62 -
Rwork0.234 1062 -
all-1124 -
obs--99.38 %

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