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- PDB-8es5: Aha1 domain protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 8es5
TitleAha1 domain protein from Pseudomonas aeruginosa
ComponentsActivator of HSP90 ATPase
KeywordsUNKNOWN FUNCTION / Uncharacterized proteins
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily / Activator of HSP90 ATPase
Function and homology information
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsColautti, J. / Whitney, J.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-175011 Canada
CitationJournal: Mol.Microbiol. / Year: 2023
Title: Lack of evidence that Pseudomonas aeruginosa AmpDh3-PA0808 constitute a type VI secretion system effector-immunity pair.
Authors: Colautti, J. / Bullen, N.P. / Whitney, J.C.
History
DepositionOct 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activator of HSP90 ATPase
B: Activator of HSP90 ATPase


Theoretical massNumber of molelcules
Total (without water)37,2562
Polymers37,2562
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.250, 80.770, 161.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

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Components

#1: Protein Activator of HSP90 ATPase / Aha-domain containing protein / Hydrophobic ligand-binding SRPBCC domain-containing protein / ...Aha-domain containing protein / Hydrophobic ligand-binding SRPBCC domain-containing protein / Polyketide cyclase


Mass: 18628.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria)
Gene: ALP65_01635, CAZ10_12280, CGU42_24225, E4V10_11310, E5D53_09975, ECC04_025130, GNQ48_22815, GUL26_32225, IPC112_06470, IPC113_16175, IPC114_06300, IPC115_16635, IPC116_21530, IPC117_23830, ...Gene: ALP65_01635, CAZ10_12280, CGU42_24225, E4V10_11310, E5D53_09975, ECC04_025130, GNQ48_22815, GUL26_32225, IPC112_06470, IPC113_16175, IPC114_06300, IPC115_16635, IPC116_21530, IPC117_23830, IPC118_24885, IPC119_22090, IPC120_22920, IPC121_15885, IPC122_14240, IPC123_21595, IPC127_17080, IPC128_12580, IPC129_14830, IPC1307_08390, IPC130_15985, IPC1311_05030, IPC1312_10265, IPC1313_09265, IPC1315_09230, IPC1316_28620, IPC1318_20315, IPC1321_08970, IPC1322_23855, IPC1323_24425, IPC1324_24975, IPC1325_28310, IPC1326_26955, IPC1327_26965, IPC1328_11460, IPC1330_07965, IPC1331_14515, IPC1332_07915, IPC1333_12745, IPC1334_21705, IPC1335_20030, IPC1337_13565, IPC1338_13970, IPC1339_06105, IPC1340_00685, IPC1342_19940, IPC1343_23115, IPC1345_07245, IPC1346_03305, IPC1347_03310, IPC1348_06420, IPC1349_24410, IPC137_09075, IPC141_05605, IPC142_12970, IPC143_04165, IPC1474_08160, IPC1479_23100, IPC1480_20605, IPC1481_16240, IPC1482_22755, IPC1485_20645, IPC1486_21520, IPC1487_28555, IPC1488_18465, IPC1489_25745, IPC1490_13950, IPC1491_29690, IPC1492_10880, IPC1494_24870, IPC1496_28030, IPC1498_25975, IPC1499_25640, IPC1502_29775, IPC1505_22755, IPC1506_24185, IPC1507_30140, IPC1508_08890, IPC1509_23845, IPC1510_21680, IPC1511_24065, IPC1514_13215, IPC1515_30070, IPC1516_27955, IPC1518_25615, IPC1519_18350, IPC1520_08810, IPC1521_25625, IPC1522_17760, IPC1523_10175, IPC1583_13105, IPC1584_18345, IPC1586_03650, IPC1588_18095, IPC1591_24450, IPC1593_10200, IPC1594_13515, IPC1595_12975, IPC1600_24650, IPC1603_10275, IPC1605_09630, IPC1606_09440, IPC161_18185, IPC162_05305, IPC163_12725, IPC164_03985, IPC165_12730, IPC166_14020, IPC167_12325, IPC168_09035, IPC169_12725, IPC170_03985, IPC171_03270, IPC177_20875, IPC179_27280, IPC180_28275, IPC181_29790, IPC184_20490, IPC26_11900, IPC29_03355, IPC30_27755, IPC31_29355, IPC32_19700, IPC34_03630, IPC35_03625, IPC36_07965, IPC37_27065, IPC38_26825, IPC41_08615, IPC42_15275, IPC43_05745, IPC44_00745, IPC45_00440, IPC46_12970, IPC47_09240, IPC48_17305, IPC49_09655, IPC50_11900, IPC51_17245, IPC56_22035, IPC574_22770, IPC575_22565, IPC576_10805, IPC577_20560, IPC578_20915, IPC579_18565, IPC57_23835, IPC580_19845, IPC582_21405, IPC584_19435, IPC586_09710, IPC589_06135, IPC58_23240, IPC596_15625, IPC597_18725, IPC598_15335, IPC599_12975, IPC600_15765, IPC601_18060, IPC602_15630, IPC603_24215, IPC604_25550, IPC605_21230, IPC606_28855, IPC607_17200, IPC608_16940, IPC609_08050, IPC610_20280, IPC611_25060, IPC612_29200, IPC613_08965, IPC614_25830, IPC615_04710, IPC616_29805, IPC618_12735, IPC61_15960, IPC620_07365, IPC621_16340, IPC622_13980, IPC623_23800, IPC624_25875, IPC625_17455, IPC627_19330, IPC629_16435, IPC630_18315, IPC632_18900, IPC633_13010, IPC634_20820, IPC737_22890, IPC73_23080, IPC74_22410, IPC75_00435, IPC76_01485, IPC77_21055, IPC78_18935, NCTC13621_07392, PA52Ts2_1801, PAMH19_4109
Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus / References: UniProt: A0A072ZZS8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1 M Sodium malonate, 0.1 M HEPES:NaOH, 0.5% (w/v) Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95369 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.97→40.38 Å / Num. obs: 39557 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 36.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01791 / Rpim(I) all: 0.01791 / Net I/σ(I): 17.15
Reflection shellResolution: 1.97→2.041 Å / Num. unique obs: 2215 / CC1/2: 0.855 / % possible all: 86.28

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6A

3q6a


Resolution: 1.97→40.38 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.6511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 1242 5 %
Rwork0.1934 23621 -
obs0.1952 24863 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.66 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 0 150 2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01962386
X-RAY DIFFRACTIONf_angle_d1.57743236
X-RAY DIFFRACTIONf_chiral_restr0.0969356
X-RAY DIFFRACTIONf_plane_restr0.017416
X-RAY DIFFRACTIONf_dihedral_angle_d7.1324316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.050.27681250.24152343X-RAY DIFFRACTION86.51
2.05-2.140.26131300.21412435X-RAY DIFFRACTION90.48
2.14-2.260.24311280.19992529X-RAY DIFFRACTION93.23
2.26-2.40.25781370.19892597X-RAY DIFFRACTION95.26
2.4-2.580.25851360.21462632X-RAY DIFFRACTION96.88
2.58-2.840.22981430.20822685X-RAY DIFFRACTION98.3
2.84-3.250.27371440.21822741X-RAY DIFFRACTION98.9
3.25-4.10.20071460.18042770X-RAY DIFFRACTION99.79
4.1-40.380.21321530.17592889X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 7.2232434387 Å / Origin y: 22.9800794029 Å / Origin z: 58.5398064488 Å
111213212223313233
T0.315318496259 Å20.04867886837 Å20.0276518875124 Å2-0.248966835831 Å2-0.0117157705068 Å2--0.238242884126 Å2
L2.8520874106 °20.583970207905 °20.502180078066 °2-1.49583413524 °20.201533908025 °2--1.46908821275 °2
S0.0114651650592 Å °-0.100305615532 Å °-0.0906209597891 Å °0.259891120486 Å °0.0594645258279 Å °0.0377924827544 Å °0.0611597354412 Å °0.0365669695646 Å °-0.0574945896952 Å °
Refinement TLS groupSelection details: all

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