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- PDB-4kqa: Crystal structure of the golgi casein kinase -

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Basic information

Entry
Database: PDB / ID: 4kqa
TitleCrystal structure of the golgi casein kinase
ComponentsProtein H03A11.1
KeywordsTRANSFERASE / secreted kinase
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / manganese ion binding / protein phosphorylation / non-specific serine/threonine protein kinase / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding
Similarity search - Function
FAM20, C-terminal / FAM20 / Golgi casein kinase, C-terminal, Fam20
Similarity search - Domain/homology
NICKEL (II) ION / Extracellular serine/threonine protein kinase CeFam20
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.603 Å
AuthorsXiao, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of the Golgi casein kinase.
Authors: Xiao, J. / Tagliabracci, V.S. / Wen, J. / Kim, S.A. / Dixon, J.E.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Dec 25, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein H03A11.1
B: Protein H03A11.1
C: Protein H03A11.1
D: Protein H03A11.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,11214
Polymers213,9514
Non-polymers4,16110
Water4,882271
1
A: Protein H03A11.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5574
Polymers53,4881
Non-polymers1,0703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein H03A11.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5574
Polymers53,4881
Non-polymers1,0703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein H03A11.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4993
Polymers53,4881
Non-polymers1,0112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein H03A11.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4993
Polymers53,4881
Non-polymers1,0112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.786, 157.306, 168.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments: (Selection details: chain 'D' RESTRAINED TORSIONS: 7827 Histogram of differences under limit:...)

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Components

#1: Protein
Protein H03A11.1


Mass: 53487.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_H03A11.1, H03A11.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9XTW2
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG4000, 200 mM imidazole-malate (4:1), 3 mM NiCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→46.464 Å / Num. obs: 64299

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.603→46.464 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 6135 5.02 %
Rwork0.2168 --
obs0.2187 -98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→46.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13850 0 270 271 14391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214534
X-RAY DIFFRACTIONf_angle_d0.7119576
X-RAY DIFFRACTIONf_dihedral_angle_d12.8145434
X-RAY DIFFRACTIONf_chiral_restr0.032091
X-RAY DIFFRACTIONf_plane_restr0.0042525
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11DX-RAY DIFFRACTIONPOSITIONAL
12DX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6027-2.63230.32162030.30673574X-RAY DIFFRACTION91
2.6323-2.66330.32641890.29463758X-RAY DIFFRACTION96
2.6633-2.69580.35352080.27993756X-RAY DIFFRACTION97
2.6958-2.72990.32162070.27943889X-RAY DIFFRACTION97
2.7299-2.76580.35311890.26193820X-RAY DIFFRACTION98
2.7658-2.80370.292300.24823865X-RAY DIFFRACTION99
2.8037-2.84370.29992010.25293847X-RAY DIFFRACTION98
2.8437-2.88620.30971880.25143926X-RAY DIFFRACTION99
2.8862-2.93130.282080.2453918X-RAY DIFFRACTION98
2.9313-2.97930.3141950.25273842X-RAY DIFFRACTION99
2.9793-3.03070.26262320.24833870X-RAY DIFFRACTION98
3.0307-3.08580.30231940.24393883X-RAY DIFFRACTION99
3.0858-3.14510.3032150.24953891X-RAY DIFFRACTION99
3.1451-3.20930.29822020.25183860X-RAY DIFFRACTION99
3.2093-3.27910.29112040.25333897X-RAY DIFFRACTION99
3.2791-3.35530.32121870.24373863X-RAY DIFFRACTION99
3.3553-3.43920.29272250.25033914X-RAY DIFFRACTION99
3.4392-3.53220.31571960.23873873X-RAY DIFFRACTION99
3.5322-3.63610.23281930.20783905X-RAY DIFFRACTION99
3.6361-3.75340.27342190.22053933X-RAY DIFFRACTION99
3.7534-3.88740.2511870.19473910X-RAY DIFFRACTION100
3.8874-4.0430.1942340.193896X-RAY DIFFRACTION99
4.043-4.22690.21751940.17823913X-RAY DIFFRACTION99
4.2269-4.44960.23341880.18383931X-RAY DIFFRACTION99
4.4496-4.72810.21562070.18163885X-RAY DIFFRACTION100
4.7281-5.09280.22882120.19223926X-RAY DIFFRACTION99
5.0928-5.60450.21911990.19463916X-RAY DIFFRACTION99
5.6045-6.41370.21712130.20743903X-RAY DIFFRACTION99
6.4137-8.07360.2172100.21823874X-RAY DIFFRACTION99
8.0736-46.47140.22192060.19823888X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.4164 Å / Origin y: 48.7857 Å / Origin z: 52.4373 Å
111213212223313233
T0.3261 Å2-0.0472 Å2-0.007 Å2-0.4034 Å2-0.0049 Å2--0.5801 Å2
L-0.0421 °2-0.1653 °2-0.0132 °2-0.0721 °20.0265 °2--0.0421 °2
S0.0382 Å °-0.0163 Å °-0.1639 Å °-0.0385 Å °-0.0335 Å °0.1888 Å °0.0064 Å °-0.0601 Å °-0.0077 Å °
Refinement TLS groupSelection details: all

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