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- PDB-2qnu: Crystal structure of PA0076 from Pseudomonas aeruginosa PAO1 at 2... -

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Basic information

Entry
Database: PDB / ID: 2qnu
TitleCrystal structure of PA0076 from Pseudomonas aeruginosa PAO1 at 2.05 A resolution
ComponentsUncharacterized protein PA0076
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSEUDOMONAS AERUGINOSA PA01 / Uncharacterized protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


pa0076 fold / pa0076 domain / T6S-associated protein TagF / T6S-associated protein TagF superfamily / TagF N-terminal domain, Type VI secretion system-associated / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Type VI secretion system-associated protein TagF
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsFilippova, E.V. / Chruszcz, M. / Skarina, T. / Kagan, O. / Cymborowski, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Pa0076 from Pseudomonas aeruginosa PAO1 at 2.05 A resolution.
Authors: Filippova, E.V. / Chruszcz, M. / Skarina, T. / Kagan, O. / Cymborowski, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W.
History
DepositionJul 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
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_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: Uncharacterized protein PA0076
B: Uncharacterized protein PA0076
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5096
Polymers48,1812
Non-polymers3274
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.257, 125.407, 49.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Beg label comp-ID: VAL / Refine code: 6

Dom-IDEns-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUAA4 - 2144 - 214
21GLUBB4 - 2144 - 214
12GLYAA4 - 2134 - 213
22GLYBB4 - 2134 - 213

NCS ensembles :
ID
1
2

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Components

#1: Protein Uncharacterized protein PA0076


Mass: 24090.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PAO1, 1C, PRS 101, LMG 12228 / Gene: PA0076 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q9I756
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium cacodylate, 0.2M Calcium acetate, 18% PEG 8000, 0.3M NDSB 256, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2007 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.05→46.32 Å / Num. obs: 23865 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 17.357
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.747 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→46.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.239 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1226 5.1 %RANDOM
Rwork0.183 ---
obs0.186 23865 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2---1.86 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 22 120 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223340
X-RAY DIFFRACTIONr_bond_other_d0.0010.023082
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9734551
X-RAY DIFFRACTIONr_angle_other_deg0.90637112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47222.971138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64215458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6581526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
X-RAY DIFFRACTIONr_nbd_refined0.2090.2675
X-RAY DIFFRACTIONr_nbd_other0.1920.22894
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21588
X-RAY DIFFRACTIONr_nbtor_other0.0910.21967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.2163
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4481.52529
X-RAY DIFFRACTIONr_mcbond_other0.3031.5883
X-RAY DIFFRACTIONr_mcangle_it1.68123385
X-RAY DIFFRACTIONr_scbond_it2.75731376
X-RAY DIFFRACTIONr_scangle_it44.51166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
13044loose positional0.65
23029loose positional0.565
13044loose thermal2.8410
23029loose thermal2.8110
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 53 -
Rwork0.189 1202 -
obs--100 %

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