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- PDB-2ffs: Structure of PR10-allergen-like protein PA1206 from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 2ffs
TitleStructure of PR10-allergen-like protein PA1206 from Pseudomonas aeruginosa PAO1
Componentshypothetical protein PA1206Hypothesis
Keywordsstructural genomics / unknown function / 7-STRANDED BETA SHEET / C-TERMINAL HELIX / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyAcetylaranotin biosynthesis cluster protein L / Acetylaranotin biosynthesis cluster protein L / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / : / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZimmerman, M.D. / Chruszcz, M. / Cymborowski, M.T. / Wang, S. / Kirillova, O. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. ...Zimmerman, M.D. / Chruszcz, M. / Cymborowski, M.T. / Wang, S. / Kirillova, O. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of PR10-Allergen-Like Protein PA1206 From Pseudomonas aeruginosa PAO1
Authors: Zimmerman, M.D. / Chruszcz, M. / Cymborowski, M.T. / Wang, S. / Kirillova, O. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Apr 13, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS THEORETICALLY PREDICTED TO BE THE DIMER SHOWN IN THE ASYMMETRIC UNIT, BUT HAS NOT BEEN EXPERIMENTALLY DETERMINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PA1206
B: hypothetical protein PA1206


Theoretical massNumber of molelcules
Total (without water)35,6982
Polymers35,6982
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-32 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.720, 90.720, 107.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: PHE / Refine code: 2 / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit of the protein is unknown.

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Components

#1: Protein hypothetical protein PA1206 / Hypothesis


Mass: 17848.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1206 / Plasmid: pET15b (modified) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 9947133, UniProt: Q9I4D2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 3.56 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 6M ammonium nitrate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2005
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17000 / Num. obs: 17000 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 36.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.58 / Num. unique all: 1496 / % possible all: 87

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.51 Å / D res low: 50 Å / FOM : 0.224 / FOM acentric: 0.231 / FOM centric: 0 / Reflection: 16775 / Reflection acentric: 16215 / Reflection centric: 560
Phasing MAD setR cullis acentric: 1.53 / R cullis centric: 1 / Highest resolution: 2.51 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 16215 / Reflection centric: 560
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
14.86-501.070.30.46511
8.73-14.861.060.40.330334
6.18-8.731.640.30.270647
4.78-6.181.330.20.1126964
3.9-4.781.170.10.1200285
3.29-3.92.1700282593
2.85-3.293.74003995114
2.51-2.851.71005050112
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se91.54564-0.48-0.916-0.0110
2Se82.63134-0.253-0.6480.1190
3Se194.81633-0.409-0.8340.050
4Se142.19644-0.322-0.7320.0560
5Se110.72616-0.506-0.7190.030
6Se127.6646-0.515-0.7170.1510
7Se203.58217-0.503-0.688-0.0450
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.86-500.4120.4810766511
8.73-14.860.5060.563033730334
6.18-8.730.5490.586075370647
4.78-6.180.5140.5401333126964
3.9-4.780.4360.45402087200285
3.29-3.90.190.19602918282593
2.85-3.290.1680.173041093995114
2.51-2.850.0580.059051625050112
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 16775
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.14-10059.50.82514
6.46-8.1455.80.883508
5.64-6.4655.90.9504
5.13-5.64540.917508
4.76-5.1358.70.92504
4.48-4.7655.30.933516
4.25-4.4855.70.924511
4.05-4.2556.30.897543
3.88-4.05560.889539
3.74-3.8866.80.846560
3.6-3.7462.50.81514
3.48-3.660.80.83611
3.37-3.4864.70.851645
3.27-3.3768.80.848657
3.18-3.2764.50.835684
3.1-3.1866.60.827699
3.02-3.169.70.824698
2.95-3.0273.80.817754
2.88-2.9576.10.832759
2.82-2.8875.50.791750
2.76-2.8276.60.787779
2.71-2.7679.30.77811
2.65-2.7182.90.784811
2.6-2.6583.30.732801
2.56-2.682.80.692809
2.51-2.5687.40.616786

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→31.69 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 17.712 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 874 5.2 %RANDOM
Rwork0.221 ---
all0.223 16881 --
obs0.223 16881 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.668 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å21.17 Å20 Å2
2--2.35 Å20 Å2
3----3.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 37 2253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222294
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9673124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40622.60496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53815345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8671518
X-RAY DIFFRACTIONr_chiral_restr0.1160.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021746
X-RAY DIFFRACTIONr_nbd_refined0.2250.2895
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.21
X-RAY DIFFRACTIONr_mcbond_it1.1431.51499
X-RAY DIFFRACTIONr_mcangle_it1.72422344
X-RAY DIFFRACTIONr_scbond_it3.3553900
X-RAY DIFFRACTIONr_scangle_it5.0244.5777
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
566TIGHT POSITIONAL0.080.05
480MEDIUM POSITIONAL0.40.5
566TIGHT THERMAL0.220.5
480MEDIUM THERMAL1.132
LS refinement shellResolution: 2.5→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 48 -
Rwork0.35 1003 -
obs-1051 100 %
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)
14.3080.1422-0.22761.9581-0.61153.8535-0.04470.076-0.0312-0.0411-0.11590.02030.04350.02460.1606-0.112-0.0197-0.0672-0.04890.0022-0.168794.29648.729328.4928
27.07262.98650.54993.3122-0.25264.0405-0.0541-0.0923-0.1398-0.07-0.0999-0.05350.0079-0.08870.154-0.0908-0.0106-0.05830.0189-0.0343-0.091773.431245.69218.4883
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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