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- PDB-13jg: E. coli DnaK bound to peptide PA1, structure B -

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Basic information

Entry
Database: PDB / ID: 13jg
TitleE. coli DnaK bound to peptide PA1, structure B
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / allosteric inhibition / DnaK / molecular chaperones / peptidomimetics / proteotoxic stress
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / : / protein-folding chaperone binding / ATP binding
Similarity search - Function
Chaperone DnaK / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
: / : / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsAriza-Mateos, A. / Serganov, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
National Science Foundation (NSF, United States)2143170 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Reengineering Protease Inhibitors to Disrupt Hsp70 Chaperone Function.
Authors: Richards, A. / Ariza-Mateos, A. / Ghosh, A. / Kim, M. / Sandler, S. / Yardumian, I. / Yawson, G. / Baryza, J. / Serganov, A. / Lupoli, T.J.
History
DepositionMay 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8555
Polymers23,8211
Non-polymers1,0344
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.900, 94.796, 117.444
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-816-

HOH

21A-950-

HOH

31A-994-

HOH

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Components

#1: Protein Chaperone protein DnaK / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 23820.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaK, Z0014, ECs0014 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P0A6Z0
#2: Chemical ChemComp-A1DFX / peptide PA1-A / 1-[(2S)-2-cyclohexyl-2-({(2S)-2-cyclohexyl-2-[(pyrazine-2-carbonyl)amino]acetyl}amino)acetyl]-L-prolyl-L-norvalyl-L-phenylalanine


Type: peptide-like, Peptide-like / Mass: 745.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H55N7O7 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002606
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4F and 2.4 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92019 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.52→30.19 Å / Num. obs: 33185 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.054 / Rrim(I) all: 0.116 / Net I/σ(I): 10.5
Reflection shellResolution: 1.52→1.54 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1608 / Rpim(I) all: 1.009 / Rrim(I) all: 2.189 / Rsym value: 1.938 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata reduction
PHENIX1.20.1_4487refinement
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→29.36 Å / SU ML: 0.1849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 1650 4.97 %
Rwork0.2081 31528 -
obs0.2088 33178 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.84 Å2
Refinement stepCycle: LAST / Resolution: 1.52→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 69 221 1955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731778
X-RAY DIFFRACTIONf_angle_d1.05272404
X-RAY DIFFRACTIONf_chiral_restr0.0563279
X-RAY DIFFRACTIONf_plane_restr0.016316
X-RAY DIFFRACTIONf_dihedral_angle_d13.6415251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.34791490.32652547X-RAY DIFFRACTION99.89
1.56-1.610.28921310.30092589X-RAY DIFFRACTION99.63
1.61-1.670.30951300.28322593X-RAY DIFFRACTION99.78
1.67-1.740.33341140.26892617X-RAY DIFFRACTION99.82
1.74-1.820.3081230.25042643X-RAY DIFFRACTION99.96
1.82-1.910.24941370.22872576X-RAY DIFFRACTION100
1.91-2.030.22761450.2192612X-RAY DIFFRACTION100
2.03-2.190.2391450.20172605X-RAY DIFFRACTION100
2.19-2.410.20521550.20492619X-RAY DIFFRACTION100
2.41-2.760.2171290.20672657X-RAY DIFFRACTION99.96
2.76-3.470.21821460.19852674X-RAY DIFFRACTION100
3.47-29.360.18311460.17782796X-RAY DIFFRACTION99.83
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)
10.9083988683170.09224178790420.5418591108471.502577623560.8038150438311.878942997020.04913586495630.049227183448-0.0224182406782-0.2722430454030.0617840743824-0.108972172698-0.13204127931-0.0431843989491-0.1193183660270.148967096221-0.003827348511610.05128012576090.1161475342490.01556184148840.14431388567-4.71280235167-14.9523027399-38.1006260411
20.834426700921-0.143407548690.7496489549937.840414866813.534759618042.74763430850.2311144786060.457250115132-0.100500865977-0.6142045568910.01651211975190.244675875616-0.458245476117-0.180967746272-0.1106195922181.253820183130.253365593806-0.07971198425420.3967069347970.0276991140717-0.0210736664598-12.2240524378-5.50985945765-55.7440727704
31.65272348160.07260054148941.981159825551.557356040680.9514940563459.174658510320.1157037343470.000125355418443-0.0484907119875-0.2303235261910.00888712911706-0.07377103480530.2220632297140.381830088578-0.04864906994010.1995687104510.05072329336260.008754789001190.1498160424320.003479546309060.265325264868-8.237534179484.86359334654-25.1270739309
42.303626245280.3672789986940.7498443180261.39668777310.1044440274092.822151566890.00230370782219-0.128608849444-0.04604611385150.1231496574230.02288157069920.04124624589660.0092047371192-0.00938504706031-0.03080353854930.1618390967890.03792737190270.01048449114340.212596178665-0.0422450369360.246644874198-8.99067195411.7360383999-16.8554387925
55.241428843381.906561897881.715028271255.407051612990.8945484450794.485501548530.183086170032-0.1033226719470.6103397685870.1268253853170.300815332989-0.636322527315-0.373424643880.413685216164-0.4046940734420.2317306403290.007895578127470.00405321784130.218094839091-0.07776625153510.440048044371-3.33866209977-6.19128452155-28.9715041314
Refinement TLS group

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

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 389 through 508 )A389 - 5081 - 120
22chain 'A' and (resid 509 through 522 )A509 - 522121 - 134
33chain 'A' and (resid 523 through 556 )A523 - 556135 - 168
44chain 'A' and (resid 557 through 607 )A557 - 607169 - 219
55chain 'A' and (resid 701 through 701 )B701

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