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- PDB-3uc2: Crystal structure of a DUF4426 family protein (PA0388) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 3uc2
TitleCrystal structure of a DUF4426 family protein (PA0388) from Pseudomonas aeruginosa PAO1 at 2.09 A resolution
Componentshypothetical protein with immunoglobulin-like foldHypothesis
KeywordsStructural Genomics / Unknown Function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4426 / Domain of unknown function DUF4426 / Domain of unknown function (DUF4426) / Immunoglobulin-like / Sandwich / Mainly Beta / DUF4426 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein with immunoglobulin-like fold (PA0388) from Pseudomonas aeruginosa PAO1 at 2.09 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein with immunoglobulin-like fold
B: hypothetical protein with immunoglobulin-like fold
C: hypothetical protein with immunoglobulin-like fold
D: hypothetical protein with immunoglobulin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,58215
Polymers62,5374
Non-polymers1,04511
Water3,585199
1
A: hypothetical protein with immunoglobulin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1076
Polymers15,6341
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein with immunoglobulin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7302
Polymers15,6341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein with immunoglobulin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0155
Polymers15,6341
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein with immunoglobulin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7302
Polymers15,6341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.453, 45.436, 294.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein
hypothetical protein with immunoglobulin-like fold / Hypothesis


Mass: 15634.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0388 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9I6A7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 20-139) 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.17M (NH4)2SO4, 15.0% Glycerol, 25.5% PEG-4000, No Buffer pH 4.2, 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: 0.91837,0.97916,0.97886
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.978861
ReflectionResolution: 2.09→49.083 Å / Num. obs: 36206 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 41.122 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.09-2.163.990.6192.213473337799.8
2.16-2.250.462315142374599.7
2.25-2.350.3284.214256353599.5
2.35-2.480.2555.315151373899.5
2.48-2.630.1787.414171349599.4
2.63-2.830.12110.714482356499
2.83-3.120.06518.114913367998.7
3.12-3.570.03728.614518361998.2
3.57-4.490.02639.214512366697.8
4.49-49.080.0244514343378894.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.09→49.083 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9298 / Occupancy max: 1 / Occupancy min: 0.5 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 5. THE REFINEMENT WAS RESTRAINED WITH THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1792 4.96 %RANDOM
Rwork0.211 ---
obs0.2122 36125 98.65 %-
Displacement parametersBiso max: 184.61 Å2 / Biso mean: 63.678 Å2 / Biso min: 23.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.8997 Å20 Å20 Å2
2---0.1978 Å20 Å2
3---3.0974 Å2
Refine analyzeLuzzati coordinate error obs: 0.348 Å
Refinement stepCycle: LAST / Resolution: 2.09→49.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 58 199 3915
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1745SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes566HARMONIC5
X-RAY DIFFRACTIONt_it3839HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion502SEMIHARMONIC5
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_contact4178SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3839HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5228HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion2.05
LS refinement shellResolution: 2.09→2.15 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2382 145 4.93 %
Rwork0.2101 2794 -
all0.2115 2939 -
obs--98.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.87741.8091-0.03693.47920.25153.0021-0.0970.29270.1711-0.2690.1305-0.0506-0.0138-0.1567-0.0334-0.12410.0082-0.012-0.0795-0.0098-0.088418.935820.1307147.631
27.004-2.4094-0.47147.2871-1.49464.3406-0.2933-1.0122-1.08280.10330.53740.17660.9679-0.193-0.2441-0.0995-0.0448-0.0389-0.12230.1875-0.289617.8572-1.6091179.839
31.57611.64840.16844.4125-0.91363.572-0.0166-0.11620.03360.04480.04250.2867-0.0999-0.0741-0.0259-0.1252-0.0069-0.0293-0.12280.0102-0.021613.505716.1325220.456
42.68920.84060.20392.4735-0.4023.56690.34330.5431-0.0469-0.08860.0261-0.4486-0.70811.0885-0.3694-0.1344-0.1973-0.01320.1811-0.0441-0.28232.535522.3511188.315
Refinement TLS groupSelection details: { D|20 - 139 }

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