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- PDB-4hsp: Crystal structure of a DUF3299 family protein (PA4066) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 4hsp
TitleCrystal structure of a DUF3299 family protein (PA4066) from Pseudomonas aeruginosa PAO1 at 2.45 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF11736 family protein / DUF3299 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / STRUCTURAL GENOMICS UNKNOWN FUNCTION
Function / homologyProtein of unknown function (DUF3299) / Protein of unknown function DUF3299 / Protein of unknown function (DUF3299) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / DUF3299 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PA4066) from Pseudomonas aeruginosa PAO1 at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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 1.5Oct 30, 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)16,69212
Polymers15,9751
Non-polymers71711
Water1,24369
1
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,76648
Polymers63,8994
Non-polymers2,86744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area14050 Å2
ΔGint28 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.033, 119.033, 60.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein hypothetical protein


Mass: 15974.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: NP_252755.1, PA4066 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9HWW2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-172 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: 3.9 Å3/Da / Density % sol: 68.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium chloride, 2.0M ammonium sulfate, 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: ALS / Beamline: 8.2.2 / Wavelength: 0.979111,0.979338,0.918401
DetectorType: ADSC Q315 / Detector: CCD / Date: Sep 20, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791111
20.9793381
30.9184011
ReflectionResolution: 2.45→29.234 Å / Num. obs: 9810 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 69.284 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.37
Reflection shell

Rmerge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.45-2.541.611402178496.3
2.54-2.641.913330172799
2.64-2.763.813827177699.8
2.76-2.95.413421172799.9
2.9-3.089.2137631768100
3.08-3.3214.8140861811100
3.32-3.6521.4138061774100
3.65-4.1831.8140931818100
4.18-5.2539136641779100
5.2543.113932182699.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.45→29.234 Å / Cor.coef. Fo:Fc: 0.9609 / Cor.coef. Fo:Fc free: 0.9378 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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. EXPERIMENTAL (MAD) PHASE RESTRAINTS WERE USED DURING REFINEMENT. 5. SULFATE (SO4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 469 4.8 %RANDOM
Rwork0.173 ---
obs0.1749 9776 99.85 %-
Displacement parametersBiso max: 159.93 Å2 / Biso mean: 66.2655 Å2 / Biso min: 34.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.0792 Å20 Å20 Å2
2---2.0792 Å20 Å2
3---4.1584 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: LAST / Resolution: 2.45→29.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 45 69 1231
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d510SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes167HARMONIC5
X-RAY DIFFRACTIONt_it1192HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion151SEMIHARMONIC5
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_contact1329SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1192HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1619HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion2.78
LS refinement shellResolution: 2.45→2.74 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2981 136 5.06 %
Rwork0.2173 2552 -
all0.2211 2688 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 71.0428 Å / Origin y: 15.1423 Å / Origin z: 3.0875 Å
111213212223313233
T0.153 Å20.0861 Å2-0.1574 Å2--0.1731 Å2-0.1196 Å2---0.0551 Å2
L1.979 °2-0.0732 °2-0.774 °2-1.6508 °20.0638 °2--2.9795 °2
S-0.2712 Å °-0.1791 Å °-0.1735 Å °0.1265 Å °0.4828 Å °-0.2601 Å °0.4982 Å °0.3689 Å °-0.2116 Å °
Refinement TLS groupSelection details: { A|0 - A|171 }

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