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- PDB-5gza: protein O-mannose kinase -

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Basic information

Entry
Database: PDB / ID: 5gza
Titleprotein O-mannose kinase
ComponentsProtein O-mannose kinase
KeywordsTRANSFERASE / protein O-mannose kinase
Function / homology
Function and homology information


O-linked glycosylation / glycoprotein-mannosyl O6-kinase / carbohydrate kinase activity / muscle structure development / swimming / phosphotransferase activity, alcohol group as acceptor / carbohydrate phosphorylation / protein O-linked glycosylation / polysaccharide binding / ADP binding ...O-linked glycosylation / glycoprotein-mannosyl O6-kinase / carbohydrate kinase activity / muscle structure development / swimming / phosphotransferase activity, alcohol group as acceptor / carbohydrate phosphorylation / protein O-linked glycosylation / polysaccharide binding / ADP binding / kinase activity / membrane => GO:0016020 / protein kinase activity / endoplasmic reticulum membrane / ATP binding
Similarity search - Function
Protein O-mannose kinase / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / 4-METHYL-2H-CHROMEN-2-ONE / Protein O-mannose kinase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsXiao, J.
CitationJournal: Elife / Year: 2016
Title: Structure of protein O-mannose kinase reveals a unique active site architecture
Authors: Zhu, Q. / Venzke, D. / Walimbe, A.S. / Anderson, M.E. / Fu, Q. / Kinch, L.N. / Wang, W. / Chen, X. / Grishin, N.V. / Huang, N. / Yu, L. / Dixon, J.E. / Campbell, K.P. / Xiao, J.
History
DepositionSep 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
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 / 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_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-mannose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1797
Polymers32,8721
Non-polymers1,3066
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-27 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 70.550, 66.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Protein O-mannose kinase / POMK / Protein kinase-like protein SgK196 / Sugen kinase 196


Mass: 32872.496 Da / Num. of mol.: 1 / Fragment: UNP residues 53-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pomk, sgk196 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5U3W1, glycoprotein-mannosyl O6-kinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGlcpNAcb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 5 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Chemical ChemComp-ZZ1 / 4-METHYL-2H-CHROMEN-2-ONE / 4-METHYLUMBELLIFERYL


Mass: 160.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O2

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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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium acetate, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2→50 Å / Num. obs: 25224 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.117 / Net I/av σ(I): 24.36 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.037.90.5140.8021100
2.03-2.0780.5060.787199.9
2.07-2.1180.4110.8861100
2.11-2.1580.3160.9241100
2.15-2.27.90.2710.9361100
2.2-2.257.80.2860.9221100
2.25-2.317.20.2350.9431100
2.31-2.377.70.2080.9571100
2.37-2.4480.1830.9731100
2.44-2.528.20.170.9711100
2.52-2.6180.1540.9751100
2.61-2.717.80.150.9741100
2.71-2.847.40.1330.9761100
2.84-2.998.10.1310.9781100
2.99-3.178.10.1250.9831100
3.17-3.4280.1220.9831100
3.42-3.767.50.1110.9821100
3.76-4.318.20.1070.9851100
4.31-5.437.80.1070.9871100
5.43-5080.1080.989199.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→35.275 Å / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.21
RfactorNum. reflection% reflection
Rfree0.2183 1240 4.93 %
Rwork0.1968 --
obs0.2032 25148 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.79 Å2 / Biso mean: 52.2548 Å2 / Biso min: 29.9 Å2
Refinement stepCycle: final / Resolution: 2→35.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 85 0 2393
Biso mean--50.28 --
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092457
X-RAY DIFFRACTIONf_angle_d1.1373332
X-RAY DIFFRACTIONf_chiral_restr0.051367
X-RAY DIFFRACTIONf_plane_restr0.004415
X-RAY DIFFRACTIONf_dihedral_angle_d17.857883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9994-2.07940.27591400.31092692283295
2.0794-2.17390.28711360.2862637277395
2.1739-2.28840.26791380.29552616275494
2.2884-2.43160.25711400.27642660280094
2.4316-2.61910.31931380.26122648278695
2.6191-2.88210.23081290.24952659278895
2.8821-3.2980.2761440.2332662280695
3.298-4.15040.21291340.18772663279795
4.1504-21.83150.17841390.14042658279795
Refinement TLS params.Method: refined / Origin x: 50.2655 Å / Origin y: 40.8287 Å / Origin z: -8.3083 Å
111213212223313233
T0.2683 Å2-0.019 Å20.0086 Å2-0.2668 Å2-0.0031 Å2--0.2924 Å2
L1.574 °2-0.1043 °2-0.2674 °2-1.4539 °20.2651 °2--1.6338 °2
S-0.007 Å °0.0229 Å °-0.1723 Å °0.0183 Å °-0.0912 Å °0.2271 Å °0.1028 Å °0.03 Å °0.0997 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA53 - 342
2X-RAY DIFFRACTION1allA381 - 403

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