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- PDB-3niz: Cryptosporidium parvum cyclin-dependent kinase cgd5_2510 with ADP... -

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Basic information

Entry
Database: PDB / ID: 3niz
TitleCryptosporidium parvum cyclin-dependent kinase cgd5_2510 with ADP bound.
ComponentsRhodanese family protein
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / phosphotransferase / cyclin dependent kinase
Function / homology
Function and homology information


[RNA-polymerase]-subunit kinase / synaptic vesicle transport / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / vesicle-mediated transport / axonogenesis / cell cycle / phosphorylation / cell division / ATP binding ...[RNA-polymerase]-subunit kinase / synaptic vesicle transport / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / vesicle-mediated transport / axonogenesis / cell cycle / phosphorylation / cell division / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cyclin-dependent kinase 2 homolog
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsWernimont, A.K. / Dong, A. / Lew, J. / Lin, Y.H. / Hassanali, A. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Wernimont, A.K. / Dong, A. / Lew, J. / Lin, Y.H. / Hassanali, A. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Cryptosporidium parvum cyclin-dependent kinase cgd5_2510 with ADP bound.
Authors: Wernimont, A.K. / Dong, A. / Lew, J. / Lin, Y.H. / Hassanali, A. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Hui, R. / Artz, J.D.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Source and taxonomy
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Rhodanese family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3244
Polymers35,8481
Non-polymers4763
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhodanese family protein
hetero molecules

A: Rhodanese family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6488
Polymers71,6972
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3770 Å2
ΔGint-70 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.337, 64.337, 200.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Rhodanese family protein


Mass: 35848.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: CGD5_2510 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CRJ8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 3350 0.15 M MgAcet 15 % ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 25615 / Num. obs: 24975 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.4 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.42 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.186.80.3722.720151.03180.8
2.18-2.268.20.36523850.9795.1
2.26-2.3710.70.31424780.98999.2
2.37-2.49130.2624990.996100
2.49-2.6514.20.20225241.058100
2.65-2.8514.40.14425281.356100
2.85-3.1414.40.10625581.609100
3.14-3.5914.30.06225711.537100
3.59-4.5213.80.05826172.464100
4.52-5012.90.03828001.54299.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9186 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 872 5.05 %RANDOM
Rwork0.2208 ---
obs0.2225 17256 --
all-17694 --
Displacement parametersBiso max: 151.05 Å2 / Biso mean: 64.6015 Å2 / Biso min: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1--5.522 Å20 Å20 Å2
2---5.522 Å20 Å2
3---11.0439 Å2
Refine analyzeLuzzati coordinate error obs: 0.362 Å
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 29 67 2348
LS refinement shellResolution: 2.4→2.54 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.328 136 5.03 %
Rwork0.2628 2568 -
all0.2659 2704 -

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