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- PDB-8wzd: The Crystal Structure of PKCi from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wzd
TitleThe Crystal Structure of PKCi from Biortus
ComponentsAdenosine 5'-monophosphoramidase HINT1
KeywordsHYDROLASE / Histidine triad nucleotide-binding protein 1 / Protein kinase C-interacting protein 1
Function / homology
Function and homology information


purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily
Similarity search - Domain/homology
Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PKCi from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
History
DepositionNov 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine 5'-monophosphoramidase HINT1
B: Adenosine 5'-monophosphoramidase HINT1


Theoretical massNumber of molelcules
Total (without water)27,5142
Polymers27,5142
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-16 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.760, 75.047, 80.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 12 - 125 / Label seq-ID: 12 - 125

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Adenosine 5'-monophosphoramidase HINT1 / Desumoylating isopeptidase HINT1 / Histidine triad nucleotide-binding protein 1 / Protein kinase C ...Desumoylating isopeptidase HINT1 / Histidine triad nucleotide-binding protein 1 / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 13756.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49773, Hydrolases; Acting on phosphorus-nitrogen bonds, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na2tartrate, 0.1M Hepes pH7.0, 20% SOKALAN PA25 CL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 2.05→45.76 Å / Num. obs: 17997 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.9
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.942 / Num. unique obs: 1368

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→40.165 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.785 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2172 1014 5.65 %
Rwork0.1705 16934 -
all0.173 --
obs-17948 99.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.127 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å2-0 Å20 Å2
2--3.639 Å2-0 Å2
3----1.378 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 0 207 1986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161703
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6472459
X-RAY DIFFRACTIONr_angle_other_deg0.4531.5843977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.295510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9210314
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6641078
X-RAY DIFFRACTIONr_chiral_restr0.0680.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined0.1940.2387
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21637
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2896
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.28
X-RAY DIFFRACTIONr_nbd_other0.1660.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.215
X-RAY DIFFRACTIONr_mcbond_it2.1212.971922
X-RAY DIFFRACTIONr_mcbond_other2.1222.971921
X-RAY DIFFRACTIONr_mcangle_it2.9524.4421149
X-RAY DIFFRACTIONr_mcangle_other2.9514.4421150
X-RAY DIFFRACTIONr_scbond_it3.253.258899
X-RAY DIFFRACTIONr_scbond_other3.2493.258899
X-RAY DIFFRACTIONr_scangle_it4.6474.7741310
X-RAY DIFFRACTIONr_scangle_other4.6454.7741311
X-RAY DIFFRACTIONr_lrange_it5.87842.6742102
X-RAY DIFFRACTIONr_lrange_other5.77839.7572052
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.053288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.116820.05009
12AX-RAY DIFFRACTIONLocal ncs0.116820.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.05-2.1030.228700.25312320.25113030.9490.93799.92330.225
2.103-2.1610.299690.24911960.25212650.9250.9411000.219
2.161-2.2230.27630.2311590.23212220.9370.951000.199
2.223-2.2910.255700.21411520.21612230.9560.95999.91820.182
2.291-2.3660.257530.20610910.20911440.940.9641000.175
2.366-2.4490.219430.18510930.18611360.9640.9711000.154
2.449-2.5410.245640.19210340.19510990.9660.97299.9090.156
2.541-2.6440.241520.1849910.18710430.9660.9761000.155
2.644-2.7610.266560.1799620.18410180.9630.9791000.151
2.761-2.8950.178550.1629170.1639720.9770.9821000.141
2.895-3.0510.242560.1688740.1739300.9660.9811000.148
3.051-3.2350.213680.1627970.1658650.9670.9841000.145
3.235-3.4570.216550.157750.1548300.9720.9851000.14
3.457-3.7320.168580.1437150.1457740.9830.98899.87080.137
3.732-4.0840.177430.1416780.1447210.9860.9881000.137
4.084-4.560.172360.1246220.1266590.9840.9999.84830.125
4.56-5.2550.194340.1185410.1215770.9860.99299.65340.122
5.255-6.4080.232310.1684800.1715120.9730.98399.80470.166
6.408-8.9490.269240.1873850.1914090.9590.9791000.19
8.949-40.1650.209140.2042410.2042570.9610.9799.22180.226

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