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- PDB-3i38: Structure of a putative chaperone protein dnaj from klebsiella pn... -

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Basic information

Entry
Database: PDB / ID: 3i38
TitleStructure of a putative chaperone protein dnaj from klebsiella pneumoniae subsp. pneumoniae mgh 78578
ComponentsPutative chaperone DnaJ
KeywordsCHAPERONE / DNAJ / KLEBSIELLA PNEUMONIAE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


bent DNA binding / nucleoid / unfolded protein binding / protein folding / cytoplasm
Similarity search - Function
DNA-binding protein, curved-DNA / Single helix bin / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain ...DNA-binding protein, curved-DNA / Single helix bin / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Curved DNA-binding protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Bearden, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a Putative Chaperone Protein Dnaj from Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Bearden, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative chaperone DnaJ
B: Putative chaperone DnaJ
C: Putative chaperone DnaJ
D: Putative chaperone DnaJ
E: Putative chaperone DnaJ
F: Putative chaperone DnaJ
G: Putative chaperone DnaJ
H: Putative chaperone DnaJ
I: Putative chaperone DnaJ
J: Putative chaperone DnaJ
K: Putative chaperone DnaJ
L: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)142,17212
Polymers142,17212
Non-polymers00
Water3,351186
1
A: Putative chaperone DnaJ
B: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-40 kcal/mol
Surface area11720 Å2
MethodPISA
2
C: Putative chaperone DnaJ
D: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-37 kcal/mol
Surface area11300 Å2
MethodPISA
3
E: Putative chaperone DnaJ
F: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-39 kcal/mol
Surface area11090 Å2
MethodPISA
4
G: Putative chaperone DnaJ
H: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-39 kcal/mol
Surface area11380 Å2
MethodPISA
5
I: Putative chaperone DnaJ
J: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-39 kcal/mol
Surface area11160 Å2
MethodPISA
6
K: Putative chaperone DnaJ
L: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-38 kcal/mol
Surface area11380 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.805, 61.626, 92.907
Angle α, β, γ (deg.)81.75, 78.71, 83.79
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13C
23D
14C
24D
15E
25F
16E
26F
17G
27H
18G
28H
19I
29J
110I
210J
111K
211L
112K
212L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A200 - 269
2114B200 - 269
1124A270 - 302
2124B270 - 302
1134C200 - 269
2134D200 - 269
1144C270 - 302
2144D270 - 302
1154E200 - 269
2154F200 - 269
1164E270 - 302
2164F270 - 302
1174G20 - 269
2174H20 - 269
1184G270 - 302
2184H270 - 302
1194I200 - 269
2194J200 - 269
11104I270 - 302
21104J270 - 302
11114K200 - 269
21114L200 - 269
11124K200 - 302
21124L200 - 302

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
DetailsAUTHORS HAD THE FOLLOWING COMMENTS ON THE SUPERHELICCAL STRUCTURE IN ASYMMETRIC UNIT: FIRST OF ALL, THE PROTEIN IS A SMALL PART OF A LARGE PROTEIN WHICH CONSISTS OF THREE DOMAINS. THEREFORE IT IS HARD TO PREDICT WHETHER THE FULL LENGTH PROTEIN WILL FORM A SIMILAR SUPERHELICAL STRUCTURE. LIGHT SCATTERING ANALYSIS CONFIRMS THAT THE PROTEIN DOMAIN FORMS A DIMER IN SOLUTION. AUTHORS ASSUME THAT THE SUPERHELICAL STRUCTURE IS AN ARTIFACT AND CREATED BY CRYSTAL PACKING. THIS IS THE VERY INTERESTING PATTERN BUT FROM FUNCTIONAL POINT OF VIEW WE DO NOT KNOW IF IT IS PHYSIOLOGICALLY RELEVANT.

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Components

#1: Protein
Putative chaperone DnaJ


Mass: 11847.640 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Gene: cbpA, KPN78578_44400, KPN_04509 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21Magic / References: UniProt: A6TH30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorDetector: CCD / Date: Jun 18, 2009 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→90.54 Å / Num. obs: 66358 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 30.081
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2 / Rsym value: 0.559 / % possible all: 97.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
CCP4model building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0051refinement
ADSCdata collection
HKL-2000data scaling
DMphasing
RESOLVEphasing
ARPWARPmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→90.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 18.451 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2941 5.1 %RANDOM
Rwork0.217 ---
obs0.219 57758 98.09 %-
all-57758 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-1.77 Å21.29 Å2
2---1.03 Å20.8 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→90.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9275 0 0 186 9461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229541
X-RAY DIFFRACTIONr_bond_other_d0.0010.026616
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.98412990
X-RAY DIFFRACTIONr_angle_other_deg0.893316299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.52451193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53924.066332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.584151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9211549
X-RAY DIFFRACTIONr_chiral_restr0.0980.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9861.56046
X-RAY DIFFRACTIONr_mcbond_other0.2741.52393
X-RAY DIFFRACTIONr_mcangle_it1.74629789
X-RAY DIFFRACTIONr_scbond_it2.59433495
X-RAY DIFFRACTIONr_scangle_it4.1234.53199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A845MEDIUM POSITIONAL0.440.5
1A845MEDIUM THERMAL0.732
2A454MEDIUM POSITIONAL0.40.5
2A454MEDIUM THERMAL1.112
3C800MEDIUM POSITIONAL0.730.5
3C800MEDIUM THERMAL0.882
4C474MEDIUM POSITIONAL0.490.5
4C474MEDIUM THERMAL0.952
5E815MEDIUM POSITIONAL0.660.5
5E815MEDIUM THERMAL0.782
6E474MEDIUM POSITIONAL0.530.5
6E474MEDIUM THERMAL0.812
7G826MEDIUM POSITIONAL0.440.5
7G826MEDIUM THERMAL0.952
8G462MEDIUM POSITIONAL0.630.5
8G462MEDIUM THERMAL1.22
9I782MEDIUM POSITIONAL0.760.5
9I782MEDIUM THERMAL0.752
10I474MEDIUM POSITIONAL0.420.5
10I474MEDIUM THERMAL0.452
11K800MEDIUM POSITIONAL0.480.5
11K800MEDIUM THERMAL0.722
12K474MEDIUM POSITIONAL0.680.5
12K474MEDIUM THERMAL0.912
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 221 -
Rwork0.294 4007 -
obs--97.6 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.07972.7814-0.56394.5805-2.63182.03490.03180.31810.70550.32820.1590.5811-0.3949-0.0793-0.19080.27520.14220.04330.12090.04820.2027-2.216816.74-2.4215
21.5082-0.0182-0.66363.1033-0.39365.2598-0.04160.0606-0.09670.3249-0.06360.1425-0.14740.02480.10510.10020.0605-0.00810.0827-0.02850.0886-1.404-7.21617.8213
32.07191.0233-1.92073.2984-0.219510.0038-0.15330.0088-0.1734-0.2878-0.104-0.28880.61820.46440.25730.10890.08270.03020.07390.01120.04317.8498-10.6409-9.5849
43.77841.5835-2.65411.3125-0.7257.6984-0.00820.14890.1460.1617-0.07360.2716-0.2585-0.73960.08190.19120.0990.02070.1734-0.04210.1264-5.8264-0.15259.0767
52.4134-1.6530.7128.0514-3.00086.0135-0.2474-0.26210.18390.15280.2410.27140.7244-0.49260.00630.1625-0.0119-0.02220.1299-0.09780.331213.2311-26.862217.289
67.1585-3.1556-0.40523.0322-3.1349.6703-0.11861.041.7062-0.3335-0.0454-0.53110.4753-0.55920.1640.1479-0.1241-0.17740.35410.24010.996227.1161-10.93634.3446
77.1107-1.49541.3955.1011-1.29061.6975-0.06120.1940.3003-0.0613-0.03870.17250.13060.04330.10.02320.0137-0.02990.0469-0.04890.164341.761-24.155710.5196
85.637-3.1940.11742.8474-1.11571.0761-0.1193-0.04510.61250.30030.092-0.2659-0.2412-0.06210.02730.09440.0603-0.07380.1094-0.04580.676619.4291-11.16937.9927
92.5161.84160.38783.83560.10152.0423-0.28410.27110.50940.03260.09931.13970.3746-0.10640.18470.2669-0.08280.08010.37510.12530.637-24.5326-3.3469-24.7634
105.9263-2.59881.29034.837-4.43575.11320.10570.61010.2464-0.9040.65380.81520.363-0.5815-0.75960.6044-0.3761-0.29450.56140.35130.3654-11.73612.5554-38.7666
114.7024-1.77792.26636.2301-3.08694.4748-0.11820.6771-0.0318-0.77180.22410.12730.72490.0299-0.10590.3221-0.1113-0.00560.29290.02670.00913.0560.8224-33.6448
124.9366-2.1458-1.30846.84330.59514.26070.14780.3388-0.1216-0.64640.4841.7537-0.0691-0.7995-0.63180.3211-0.3082-0.27290.62720.4720.6844-19.083812.3672-34.8683
139.1463-1.4178-1.29532.517-0.26833.04880.1825-0.23590.52220.301-0.06890.1159-0.40180.0438-0.11360.22360.03080.01510.0341-0.03320.0516-26.4798-12.4067-58.4564
145.281-2.2884-0.6763.33451.45682.78140.2359-0.2808-0.64270.098-0.3504-0.00140.07730.3880.11460.1372-0.0196-0.04690.28160.13950.1257-6.5695-27.5236-51.4635
154.656-1.1445-5.45722.97282.17297.34710.1008-0.69490.09590.5885-0.04620.2404-0.2830.6394-0.05460.3401-0.05710.01880.4930.13690.1841-15.7628-26.7546-33.5116
168.4808-0.7763-0.55943.4689-1.82953.89230.49990.0866-0.40360.2222-0.6954-0.1574-0.23520.9450.19550.1620.007-0.03450.2970.05220.0328-8.5704-22.5212-57.755
179.68250.8329-3.24683.6521.1066.7811-0.5334-0.3657-1.46940.46730.4794-0.11120.37760.40950.0540.53510.1423-0.02430.1765-0.0970.505923.305-50.503211.381
181.4337-1.62731.30721.888-1.67592.1205-0.044-0.0790.72090.0472-0.0829-0.7186-0.24610.62280.12690.3806-0.20810.17120.6323-0.37430.664331.5413-49.3705-11.3846
1910.0287-4.35461.24245.9162-0.22440.6974-0.13280.67910.7146-0.68060.2541-0.3859-0.35940.2422-0.12140.3854-0.18130.11480.3391-0.04360.139214.3131-39.4807-14.0474
200.59110.3332-0.97280.4099-0.40561.7336-0.2075-0.0141-0.36870.0779-0.0833-0.460.2330.12070.29090.4526-0.11150.03730.5061-0.3420.780833.2081-53.472-4.3222
213.16230.5917-2.16371.9493-1.34219.415-0.1778-0.2901-0.4888-0.0581-0.2814-0.54910.34580.80130.45920.08570.0779-0.02320.1740.09970.2601-36.9997-47.2707-56.5807
221.7879-0.1249-0.0553.82070.35772.33460.1574-0.3436-0.09660.69090.01010.18710.0554-0.1401-0.16750.3420.0018-0.02620.31140.06070.0489-54.1474-38.4316-39.63
234.982.3269-0.7376.2965-1.23892.14970.1457-0.27110.46940.14440.10420.2844-0.1586-0.1545-0.24990.14670.09880.00910.191-0.00960.0636-49.661-21.4845-47.633
241.25040.0997-1.17732.44230.50545.1228-0.0895-0.29140.02910.4625-0.0455-0.20390.5117-0.22410.1350.2803-0.0133-0.08470.31130.07910.1249-49.9578-45.3496-40.8003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A200 - 269
2X-RAY DIFFRACTION2A270 - 302
3X-RAY DIFFRACTION3B200 - 269
4X-RAY DIFFRACTION4B270 - 302
5X-RAY DIFFRACTION5C201 - 269
6X-RAY DIFFRACTION6C270 - 302
7X-RAY DIFFRACTION7D200 - 269
8X-RAY DIFFRACTION8D270 - 302
9X-RAY DIFFRACTION9E201 - 269
10X-RAY DIFFRACTION10E270 - 302
11X-RAY DIFFRACTION11F200 - 269
12X-RAY DIFFRACTION12F270 - 302
13X-RAY DIFFRACTION13G200 - 269
14X-RAY DIFFRACTION14G270 - 302
15X-RAY DIFFRACTION15H202 - 269
16X-RAY DIFFRACTION16H270 - 302
17X-RAY DIFFRACTION17I201 - 269
18X-RAY DIFFRACTION18I270 - 302
19X-RAY DIFFRACTION19J200 - 269
20X-RAY DIFFRACTION20J270 - 302
21X-RAY DIFFRACTION21K200 - 269
22X-RAY DIFFRACTION22K270 - 302
23X-RAY DIFFRACTION23L201 - 269
24X-RAY DIFFRACTION24L270 - 302

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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