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- PDB-3dob: Peptide-binding domain of Heat shock 70 kDa protein F44E5.5 from ... -

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Basic information

Entry
Database: PDB / ID: 3dob
TitlePeptide-binding domain of Heat shock 70 kDa protein F44E5.5 from C.elegans.
ComponentsHeat shock 70 kDa protein F44E5.5
KeywordsPROTEIN BINDING / structural genomics / APC90015.11 / Peptide-binding domain / Hsp70 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding
Function / homologySubstrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Sandwich / Mainly Beta / BETA-MERCAPTOETHANOL / :
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsOsipiuk, J. / Hatzos, C. / Gu, M. / Zhang, R. / Voisine, C. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of Peptide-binding domain of Heat shock 70 kDa protein F44E5.5 from C.elegans.
Authors: OSIPIUK, J. / HATZOS, C. / GU, M. / ZHANG, R. / VOISINE, C. / MORIMOTO, R.I. / JOACHIMIAK, A.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock 70 kDa protein F44E5.5
B: Heat shock 70 kDa protein F44E5.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7944
Polymers33,6372
Non-polymers1562
Water1,946108
1
A: Heat shock 70 kDa protein F44E5.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8972
Polymers16,8191
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock 70 kDa protein F44E5.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8972
Polymers16,8191
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.009, 102.009, 80.678
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsputative monomer

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Components

#1: Protein Heat shock 70 kDa protein F44E5.5


Mass: 16818.658 Da / Num. of mol.: 2 / Fragment: Peptide-binding domain, residues 369-544 / Mutation: D480N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: F44E5.4, F44E5.5 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XTL8
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.6 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 50 mM Tris buffer, 0.8 M ammonium sulfate, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.39→38.8 Å / Num. all: 19448 / Num. obs: 19448 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.158 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.85 / Num. unique all: 1905 / Χ2: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2op6.pdb

2op6


Resolution: 2.39→38.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.847 / SU B: 11.171 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.252 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1991 10.3 %RANDOM
Rwork0.184 ---
all0.188 19424 --
obs0.188 19424 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.85 Å2 / Biso mean: 46.3 Å2 / Biso min: 24.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.39→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 8 108 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222309
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9623113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99224.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53715413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1011523
X-RAY DIFFRACTIONr_chiral_restr0.110.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021771
X-RAY DIFFRACTIONr_nbd_refined0.2250.2920
X-RAY DIFFRACTIONr_nbtor_refined0.30.21530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.26
X-RAY DIFFRACTIONr_mcbond_it0.7811.51501
X-RAY DIFFRACTIONr_mcangle_it1.31322355
X-RAY DIFFRACTIONr_scbond_it2.1113884
X-RAY DIFFRACTIONr_scangle_it3.2234.5758
LS refinement shellResolution: 2.395→2.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 133 -
Rwork0.258 1266 -
all-1399 -
obs-1399 98.11 %
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)
11.6378-3.8382-0.333413.69733.94692.99670.02370.17580.1906-0.2614-0.0023-0.13940.2860.0908-0.02150.1983-0.02120.04540.002-0.0314-0.06747.98414.252-4.9896
20.9468-1.2976-0.02082.61470.79490.7026-0.04760.0270.0368-0.14570.03240.1721-0.06840.06120.01530.1562-0.00910.018-0.0482-0.00770.010747.423712.30126.444
33.28250.0165-2.53353.7179-6.036115.32210.16350.3-0.0584-0.28740.11820.4893-0.0966-0.4169-0.28180.1088-0.0273-0.0892-0.0695-0.0148-0.022340.60289.844-5.7251
41.10960.59481.22596.42563.19412.83240.05390.0857-0.11240.22110.1276-0.15450.0474-0.1222-0.18150.1292-0.00440.0451-0.0672-0.04240.024946.7198.40389.6346
50.88380.20850.2731.4771-0.55824.93290.02150.15-0.0579-0.09170.15470.04190.4366-0.0035-0.17620.08690.00570.0161-0.0482-0.04410.057841.41453.12138.4694
67.10647.62044.695231.78633.1626.41810.00781.05390.697-1.89690.30941.2720.36560.1725-0.31720.2557-0.0711-0.02640.0258-0.0399-0.289446.30299.5845-17.3316
74.7679-2.134-2.037.8371-4.29147.8980.0471-0.00131.2389-0.44810.2952-0.7219-0.75690.121-0.34230.1775-0.0730.1226-0.09760.05550.181450.490320.2017-0.3203
83.7316-0.8402-3.17971.3885-0.1243.29770.10270.38380.2345-0.1242-0.2156-0.0406-0.14640.04140.11290.1468-0.07770.0985-0.0607-0.02960.024662.866810.9953-1.6821
90.78831.69620.10553.86070.8591.9066-0.19870.1572-0.05-0.34910.1259-0.03260.1190.31010.07280.08360.01580.08620.0092-0.0507-0.026963.7358-2.6219-0.6073
103.26130.0423-4.42625.2937-7.866217.52710.2540.34160.4298-0.1363-0.3535-0.3447-0.85491.14820.09960.0611-0.11020.17970.0451-0.02680.025969.64279.1927-9.0575
112.37892.47081.10533.24680.08842.1632-0.18390.1160.2511-0.17020.03660.16560.15850.49740.14730.07720.00620.07250.039-0.07540.047864.9724-2.17984.3023
127.52811.55980.0646.05411.65167.3445-0.13110.39570.2669-0.54780.1581-0.4652-0.26570.5843-0.027-0.0210.1090.00810.0372-0.05660.033167.626-2.06038.7037
136.28854.9994.97056.27364.746813.37690.41680.2401-0.46030.0152-0.432-0.90161.11850.40250.01510.1137-0.02330.0108-0.05570.10290.076268.367918.2198-10.7193
149.18536.69232.665512.8753-11.055121.8907-0.34281.1390.0097-1.14060.82550.86250.21991.1026-0.48260.4033-0.07410.08750.0108-0.1249-0.111260.157-0.9105-12.5921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA396 - 4204 - 28
2X-RAY DIFFRACTION2AA421 - 44329 - 51
3X-RAY DIFFRACTION3AA444 - 46052 - 68
4X-RAY DIFFRACTION4AA461 - 49369 - 101
5X-RAY DIFFRACTION5AA494 - 512102 - 120
6X-RAY DIFFRACTION6AA513 - 535121 - 143
7X-RAY DIFFRACTION7AA536 - 544144 - 152
8X-RAY DIFFRACTION8BB395 - 4203 - 28
9X-RAY DIFFRACTION9BB421 - 44429 - 52
10X-RAY DIFFRACTION10BB445 - 45653 - 64
11X-RAY DIFFRACTION11BB457 - 49265 - 100
12X-RAY DIFFRACTION12BB493 - 508101 - 116
13X-RAY DIFFRACTION13BB509 - 532117 - 140
14X-RAY DIFFRACTION14BB533 - 544141 - 152

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