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- PDB-5wrs: Crystal Structure of Fam20A in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 5wrs
TitleCrystal Structure of Fam20A in complex with ATP
ComponentsPseudokinase FAM20A
KeywordsTRANSFERASE / secretory pathway pseudokinase
Function / homology
Function and homology information


tooth eruption / biomineral tissue development / enamel mineralization / calcium ion homeostasis / protein serine/threonine kinase activator activity / Post-translational protein phosphorylation / response to bacterium / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / Golgi apparatus ...tooth eruption / biomineral tissue development / enamel mineralization / calcium ion homeostasis / protein serine/threonine kinase activator activity / Post-translational protein phosphorylation / response to bacterium / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / cytoplasm
Similarity search - Function
FAM20, C-terminal / FAM20 / Golgi casein kinase, C-terminal, Fam20
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Pseudokinase FAM20A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhu, Q.
CitationJournal: Elife / Year: 2017
Title: Structure of Fam20A reveals a pseudokinase featuring a unique disulfide pattern and inverted ATP-binding
Authors: Cui, J. / Zhu, Q. / Zhang, H. / Cianfrocco, M.A. / Leschziner, A.E. / Dixon, J.E. / Xiao, J.
History
DepositionDec 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
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_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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudokinase FAM20A
B: Pseudokinase FAM20A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1628
Polymers100,8562
Non-polymers2,3066
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-4 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.202, 157.202, 144.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 89 through 144 or resid 150 through 216 or resid 218 through 525))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYchain AAA89 - 5251 - 437
21SERSERMETMET(chain B and (resid 89 through 144 or resid 150 through 216 or resid 218 through 525))BB89 - 1441 - 56
22ASPASPLYSLYS(chain B and (resid 89 through 144 or resid 150 through 216 or resid 218 through 525))BB150 - 21662 - 128
23SERSERGLYGLY(chain B and (resid 89 through 144 or resid 150 through 216 or resid 218 through 525))BB218 - 525130 - 437

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Components

#1: Protein Pseudokinase FAM20A


Mass: 50428.027 Da / Num. of mol.: 2 / Fragment: UNP residues 89-526 / Mutation: N332K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM20A, UNQ9388/PRO34279 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96MK3
#2: 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.: 2
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 5.12 Å3/Da / Density % sol: 75.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: ammonium sulfate, HEPES, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 55133 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 57.05 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.75-2.810.61.470.7881100
2.8-2.8510.61.3360.8031100
2.85-2.910.61.1290.8291100
2.9-2.9610.70.8960.891100
2.96-3.0310.70.8580.891100
3.03-3.110.70.6470.9371100
3.1-3.1710.80.4930.9581100
3.17-3.2610.90.4110.9671100
3.26-3.3610.90.3730.9691100
3.36-3.4610.90.2890.9821100
3.46-3.59110.2280.9881100
3.59-3.7310.80.1970.991100
3.73-3.9110.1670.9921100
3.9-4.1110.80.1490.9941100
4.11-4.3610.80.1270.9941100
4.36-4.710.70.1240.9941100
4.7-5.1710.60.1160.9931100
5.17-5.9210.50.110.9951100
5.92-7.4610.40.0840.9971100
7.46-5010.30.0590.998198.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WRR

5wrr


Resolution: 2.75→41.943 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1946 3.61 %
Rwork0.2029 --
obs0.2042 53978 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→41.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7018 0 146 0 7164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027355
X-RAY DIFFRACTIONf_angle_d0.6149971
X-RAY DIFFRACTIONf_dihedral_angle_d12.1284457
X-RAY DIFFRACTIONf_chiral_restr0.041099
X-RAY DIFFRACTIONf_plane_restr0.0041268
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4307X-RAY DIFFRACTION9.752TORSIONAL
12B4307X-RAY DIFFRACTION9.752TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81880.35181370.29993660X-RAY DIFFRACTION100
2.8188-2.8950.29251400.27843679X-RAY DIFFRACTION100
2.895-2.98010.31951380.27363659X-RAY DIFFRACTION100
2.9801-3.07630.31821350.25763694X-RAY DIFFRACTION100
3.0763-3.18620.25481390.2313685X-RAY DIFFRACTION100
3.1862-3.31370.26061390.21923691X-RAY DIFFRACTION100
3.3137-3.46450.23731400.21463714X-RAY DIFFRACTION100
3.4645-3.6470.2341410.20233687X-RAY DIFFRACTION100
3.647-3.87540.20321390.18443704X-RAY DIFFRACTION100
3.8754-4.17430.21031380.1833723X-RAY DIFFRACTION100
4.1743-4.59390.19041390.16643709X-RAY DIFFRACTION100
4.5939-5.25760.21841400.17363759X-RAY DIFFRACTION100
5.2576-6.61980.21841350.21363785X-RAY DIFFRACTION100
6.6198-41.94740.2561460.19333883X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.6331 Å / Origin y: 66.9262 Å / Origin z: 22.5083 Å
111213212223313233
T0.315 Å20.0186 Å2-0.0103 Å2-0.6798 Å20.0113 Å2--0.701 Å2
L2.2299 °20.0504 °2-0.5034 °2-0.3588 °20.3144 °2--0.4487 °2
S0.0511 Å °0.3004 Å °-0.0557 Å °-0.0452 Å °-0.0222 Å °-0.0129 Å °0.0077 Å °0.0565 Å °-0.0336 Å °
Refinement TLS groupSelection details: all

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