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- PDB-5fpm: Structure of heat shock-related 70kDA protein 2 with small-molecu... -

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Basic information

Entry
Database: PDB / ID: 5fpm
TitleStructure of heat shock-related 70kDA protein 2 with small-molecule ligand 5-phenyl-1,3,4-oxadiazole-2-thiol (AT809) in an alternate binding site.
ComponentsHEAT SHOCK-RELATED 70KDA PROTEIN 2
KeywordsCHAPERONE / HEAT SHOCK-RELATED PROTEIN / HEAT SHOCK / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT809.
Function / homology
Function and homology information


CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / : / spermatid development ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / : / spermatid development / Regulation of HSF1-mediated heat shock response / positive regulation of G2/M transition of mitotic cell cycle / response to unfolded protein / Attenuation phase / heat shock protein binding / protein folding chaperone / Meiotic synapsis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / PKR-mediated signaling / tau protein binding / disordered domain specific binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / spermatogenesis / blood microparticle / enzyme binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / 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 ...Defensin A-like - #30 / Defensin A-like / 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, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL / Heat shock-related 70 kDa protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJhoti, H. / Ludlow, R.F. / Patel, S. / Saini, H.K. / Tickle, I.J. / Verdonk, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening.
Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H.
History
DepositionDec 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK-RELATED 70KDA PROTEIN 2
B: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1224
Polymers84,7662
Non-polymers3562
Water19,6901093
1
A: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5612
Polymers42,3831
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5612
Polymers42,3831
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 94.960, 81.540
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00174, 0.00515), (0.00169, -0.99995, 0.00959), (0.00517, -0.00958, -0.99994)
Vector: 24.189, -9.257, 40.724)

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Components

#1: Protein HEAT SHOCK-RELATED 70KDA PROTEIN 2


Mass: 42383.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P54652
#2: Chemical ChemComp-IWT / 5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL


Mass: 178.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6N2OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1093 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL (IWT): ASTEX COMPOUND REGISTRY AT809.
Sequence details3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. ...3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. RESIDUES 386-639 DELETED.

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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: 2.3 Å3/Da / Density % sol: 46.14 % / Description: NONE
Crystal growpH: 8
Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 11MG/ML.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU SATURN CCD / Detector: CCD / Date: Jun 24, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→38.4 Å / Num. obs: 53541 / % possible obs: 97.8 % / Observed criterion σ(I): -3.7 / Redundancy: 2.2 % / Biso Wilson estimate: 24.64 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 89.3

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
CSEARCHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FPD

5fpd


Resolution: 1.96→38.37 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.9282 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 2660 5.08 %RANDOM
Rwork0.1695 ---
obs0.172 52336 97.63 %-
Displacement parametersBiso mean: 26.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.1137 Å20 Å20.4079 Å2
2---0.1682 Å20 Å2
3----1.9455 Å2
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: LAST / Resolution: 1.96→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 24 1093 6893
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125904HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037982HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2068SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes155HARMONIC2
X-RAY DIFFRACTIONt_gen_planes890HARMONIC16
X-RAY DIFFRACTIONt_it5904HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.6
X-RAY DIFFRACTIONt_other_torsion15.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion803SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8099SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2385 147 4.37 %
Rwork0.1763 3220 -
all0.179 3367 -
obs--85.29 %
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)
11.5316-0.17450.33130.8735-0.31310.7546-0.013-0.0170.00670.02830.0044-0.05610.01980.04240.0086-0.03210.0126-0.017-0.0586-0.0017-0.052527.499-9.28132.716
21.15670.0090.56860.82650.07741.5827-0.05320.15910.2153-0.08530.00930.0099-0.04410.01140.0439-0.02510.0037-0.041-0.05840.04280.000715.46398.355-8.1831
32.82280.3532.11350.9890.13063-0.2275-0.31860.31360.0612-0.08970.1697-0.2516-0.22460.3172-0.02580.0313-0.0313-0.0573-0.02170.011625.013916.316519.0281
41.44590.1756-0.20810.8808-0.29220.7992-0.04250.0811-0.0371-0.01570.0098-0.0311-0.0470.00020.0327-0.0369-0.01560.003-0.0562-0.0083-0.060251.66230.10538.244
51.3674-0.7424-0.31591.15280.49531.6452-0.0471-0.1305-0.31190.11960.0270.17350.1037-0.04690.0201-0.0211-0.02150.0453-0.0670.03580.013639.6568-17.741248.7625
62.5110.583-1.20981.1409-0.19991.8628-0.15550.2178-0.0951-0.0856-0.01860.04460.0953-0.07530.1741-0.0154-0.0131-0.0128-0.0573-0.0038-0.004549.3237-25.228721.8448

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