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- PDB-8zr0: Crystal structure of Skd3 in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 8zr0
TitleCrystal structure of Skd3 in complex with AMPPNP
ComponentsCaseinolytic peptidase B protein homolog
KeywordsCHAPERONE / Disaggregase
Function / homology
Function and homology information


head development / thigmotaxis / anatomical structure morphogenesis / cerebellum development / cellular response to heat / ATP hydrolysis activity / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
: / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...: / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / ATPase, AAA-type, core / Ankyrin repeat-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitochondrial disaggregase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsLee, S. / Lee, C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9G8022417 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A2C2009550 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of Skd3 in complex with AMPPNP
Authors: Lee, S. / Lee, C.
History
DepositionJun 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caseinolytic peptidase B protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4532
Polymers60,9471
Non-polymers5061
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.699, 119.699, 89.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Caseinolytic peptidase B protein homolog / Skd3


Mass: 60946.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: clpb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8M3AT32
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 15% SOKALAN cp5, 100 mM Bis-Tris pH 6.0, 100 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16197 / % possible obs: 98.8 % / Redundancy: 9.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Χ2: 1.511 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.954.80.2987510.7380.9220.1380.330.20394.5
2.95-35.10.2697980.8840.9690.1190.2960.22994.8
3-3.065.60.2248010.9470.9860.0960.2450.24399
3.06-3.1260.2247950.9460.9860.0910.2430.27798.6
3.12-3.196.40.1978080.9720.9930.0770.2130.34798.5
3.19-3.276.60.1788050.9770.9940.0680.1920.37198.4
3.27-3.356.50.1617930.9840.9960.0620.1730.4498.3
3.35-3.447.70.1488140.9890.9970.0530.1580.57599.4
3.44-3.548.50.1298060.9930.9980.0430.1360.72299
3.54-3.6510.10.1158140.9960.9990.0350.1210.88599.5
3.65-3.78110.1068050.9970.9990.0320.1111.06899.8
3.78-3.9411.50.0968150.9970.9990.0280.11.43199.9
3.94-4.1111.70.0888180.9970.9990.0260.0921.69599.5
4.11-4.3312.60.0768070.99810.0220.0791.89999.5
4.33-4.612.80.0718260.99910.020.0742.17899.8
4.6-4.9613.10.0648140.99910.0180.0672.26699.8
4.96-5.4613.10.0588180.99910.0170.0612.09599.8
5.46-6.2412.10.0558320.99910.0160.0572.06399.6
6.24-7.8612.70.0448270.99910.0130.0462.45299.9
7.86-5014.40.0348500.99910.0090.0352.56699.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.833 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 1612 5.02 %
Rwork0.2047 --
obs0.2074 16173 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 31 3 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083968
X-RAY DIFFRACTIONf_angle_d1.3295352
X-RAY DIFFRACTIONf_dihedral_angle_d16.1651496
X-RAY DIFFRACTIONf_chiral_restr0.046596
X-RAY DIFFRACTIONf_plane_restr0.006694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.08190.39581370.35152477X-RAY DIFFRACTION96
3.0819-3.31980.34571280.28982555X-RAY DIFFRACTION99
3.3198-3.65380.27251340.24072551X-RAY DIFFRACTION99
3.6538-4.18220.27031320.20122554X-RAY DIFFRACTION100
4.1822-5.26820.24121380.19042596X-RAY DIFFRACTION100
5.2682-48.30.22011430.17282628X-RAY DIFFRACTION100
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)
11.49420.4062-0.23022.84731.51312.06810.158-0.1762-1.44620.8753-0.01320.67941.4469-0.695-0.24211.1026-0.1260.17610.86340.26591.512963.795-54.23629.826
23.779-1.34821.62742.2672-1.17041.6237-0.05680.0856-0.5170.1447-0.10820.42980.06190.08230.160.6326-0.02180.06530.58480.0510.63556.654-36.21116.025
31.61030.21031.51761.3884-0.2571.85780.29090.20011.49270.0241-0.03282.259-1.6683-1.2635-0.07190.94160.29150.09471.20080.17341.721322.688-13.7291.564
41.5190.503-0.95930.9941-1.1431.3915-0.15540.3796-0.4094-0.0910.51512.1371-0.6022-0.867-0.37290.9913-0.07870.08491.18460.26192.057415.643-18.1613.912
53.94692.1736-0.03452.2209-0.65774.03091.0159-1.0809-0.86221.25050.12750.4654-0.150.1892-0.68120.9985-0.0903-0.0780.92430.12881.241436.236-22.20617.595
60.13380.3611-0.16710.7768-0.1671.38230.3845-1.5005-0.7660.68870.6411-0.3436-1.26321.6172-0.5151.41430.0016-0.20891.54370.14431.60835.924-35.53819.604
77.4745-1.5837-2.42830.9296-0.7313.6054-0.5593-1.6139-0.4790.97120.58821.43050.3109-0.4428-0.38521.3375-0.09340.40951.069-0.12441.399424.05-20.45119.017
82.05380.88680.59874.5011-1.59612.08990.4158-0.6084-0.16690.5706-0.33080.2863-0.44680.3853-0.33930.7229-0.1249-0.08610.6925-0.28850.559650.992-5.932.617
92.72040.3566-0.70072.9469-0.69551.01160.1463-0.37930.33150.5546-0.25870.0763-0.3916-0.02210.06660.9561-0.1089-0.12320.6553-0.14481.030855.1063.5890.298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 121:175 )A121 - 175
2X-RAY DIFFRACTION2( CHAIN A AND RESID 176:343 )A176 - 343
3X-RAY DIFFRACTION3( CHAIN A AND RESID 344:381 )A344 - 381
4X-RAY DIFFRACTION4( CHAIN A AND RESID 396:446 )A396 - 446
5X-RAY DIFFRACTION5( CHAIN A AND RESID 447:477 )A447 - 477
6X-RAY DIFFRACTION6( CHAIN A AND RESID 478:501 )A478 - 501
7X-RAY DIFFRACTION7( CHAIN A AND RESID 502:529 )A502 - 529
8X-RAY DIFFRACTION8( CHAIN A AND RESID 530:574 )A530 - 574
9X-RAY DIFFRACTION9( CHAIN A AND RESID 575:628 )A575 - 628

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