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

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Basic information

Entry
Database: PDB / ID: 5fpn
TitleStructure of heat shock-related 70kDA protein 2 with small-molecule ligand 3,5-dimethyl-1H-pyrazole-4-carboxylic acid (AT9084) in an alternate binding site.
ComponentsHEAT SHOCK-RELATED 70 KDA PROTEIN 2
KeywordsSIGNALING PROTEIN / HEAT SHOCK / CHAPERONE / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT9084.
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
3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID / 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 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 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 70 KDA PROTEIN 2
B: HEAT SHOCK-RELATED 70 KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0336
Polymers140,4722
Non-polymers5614
Water14,934829
1
A: HEAT SHOCK-RELATED 70 KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5163
Polymers70,2361
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HEAT SHOCK-RELATED 70 KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5163
Polymers70,2361
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.820, 94.850, 81.870
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00084, 0.00363), (0.00083, -0.99999, 0.00383), (0.00363, -0.00383, -0.99999)
Vector: 24.293, -9.176, 40.762)

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Components

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


Mass: 70235.984 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 4-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54652
#2: Chemical
ChemComp-KYD / 3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID


Mass: 140.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID (KYD): ASTEX COMPOUND REGISTRY AT9084.
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 % / Description: NONE
Crystal growpH: 8
Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 11 MG/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: Jul 22, 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→40.9 Å / Num. obs: 53549 / % possible obs: 97 % / Observed criterion σ(I): -3.7 / Redundancy: 2.5 % / Biso Wilson estimate: 24.42 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.8
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.4 / % possible all: 81.4

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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→40.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9189 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.164 / Details: DISORDERED REGIONS WERE DELETED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 2635 5.08 %RANDOM
Rwork0.1744 ---
obs0.1773 51848 96.85 %-
Displacement parametersBiso mean: 25.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.4211 Å20 Å20.5069 Å2
2--1.6182 Å20 Å2
3----3.0392 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 1.96→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 40 829 6661
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125950HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.048052HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2085SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes153HARMONIC2
X-RAY DIFFRACTIONt_gen_planes896HARMONIC16
X-RAY DIFFRACTIONt_it5950HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.5
X-RAY DIFFRACTIONt_other_torsion16.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion804SEMIHARMONIC5
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_contact7793SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2475 144 4.7 %
Rwork0.1719 2918 -
all0.1756 3062 -
obs--77.62 %
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)
11.3026-0.08760.22330.7734-0.17530.6574-0.0084-0.03470.02110.0201-0.0062-0.03170.02570.02520.0147-0.03320.0141-0.0145-0.0503-0.0021-0.042327.6185-9.24862.7106
21.01090.10030.43830.9291-0.06781.2435-0.04570.12570.2247-0.09270.03020.0185-0.04230.01970.0155-0.02290.0063-0.0402-0.04710.030.008115.49648.4565-8.0331
32.7206-0.1481.76091.07060.05362.3291-0.1932-0.21440.27350.0306-0.07590.0971-0.152-0.14560.2692-0.03110.0141-0.0208-0.0566-0.01940.01225.112616.089219.0593
41.25780.0918-0.18740.8582-0.21220.6296-0.03380.0769-0.0432-0.01460.0092-0.0294-0.04050.01090.0246-0.0306-0.0140.0018-0.0475-0.0048-0.044551.91680.109338.2098
50.7925-0.1484-0.22461.08510.24221.4822-0.026-0.1235-0.24240.10540.02580.09130.019-0.01590.0003-0.0372-0.01160.0359-0.05130.04110.02539.8172-17.727248.7849
62.4860.6702-1.50490.7945-0.19741.7217-0.18120.2104-0.1271-0.0735-0.00690.05150.1102-0.07960.1881-0.0277-0.0122-0.0065-0.0461-0.00520.005249.5362-25.437221.6552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|188 A|368 - A|384 }
2X-RAY DIFFRACTION2{ A|192 - A|231 A|309 - A|367 }
3X-RAY DIFFRACTION3{ A|232 - A|308 }
4X-RAY DIFFRACTION4{ B|4 - B|188 B|368 - B|384 }
5X-RAY DIFFRACTION5{ B|192 - B|231 B|309 - B|367 }
6X-RAY DIFFRACTION6{ B|232 - B|308 }

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