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- PDB-5wrr: Crystal structure of Fam20A -

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Basic information

Entry
Database: PDB / ID: 5wrr
TitleCrystal structure of Fam20A
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
Model detailsCrystal Structure of Fam20A
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: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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)102,3506
Polymers100,8562
Non-polymers1,4944
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-5 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.854, 156.854, 143.655
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.: 3
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.: 1
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

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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: 5.06 Å3/Da / Density % sol: 75.68 %
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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 70256 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 53.85 Å2 / Rmerge(I) obs: 0.172 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.5411.11.8040.8411100
2.54-2.5911.21.5180.8531100
2.59-2.6411.21.4120.8611100
2.64-2.6911.21.0750.9261100
2.69-2.7511.20.9350.9411100
2.75-2.8211.20.8060.9551100
2.82-2.8911.30.6520.9631100
2.89-2.9611.30.5460.9711100
2.96-3.0511.20.4480.981100
3.05-3.1511.20.3370.9841100
3.15-3.2611.20.2730.9851100
3.26-3.3911.10.2190.991100
3.39-3.55110.170.9931100
3.55-3.7310.90.1450.9931100
3.73-3.9710.90.1290.9931100
3.97-4.2710.80.1170.994199.9
4.27-4.710.40.1110.993199.9
4.7-5.3810.30.1090.9921100
5.38-6.7810.20.0970.9951100
6.78-509.70.0880.993198.5

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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: 4KQA

4kqa


Resolution: 2.506→39.136 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1994 2.84 %
Rwork0.2154 --
obs0.2158 70179 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.506→39.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7039 0 98 0 7137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027326
X-RAY DIFFRACTIONf_angle_d0.6179939
X-RAY DIFFRACTIONf_dihedral_angle_d11.5284451
X-RAY DIFFRACTIONf_chiral_restr0.0411107
X-RAY DIFFRACTIONf_plane_restr0.0041275
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4305X-RAY DIFFRACTION9.513TORSIONAL
12B4305X-RAY DIFFRACTION9.513TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.506-2.56860.27681390.30134794X-RAY DIFFRACTION99
2.5686-2.63810.35041390.28524792X-RAY DIFFRACTION100
2.6381-2.71570.30471390.27164852X-RAY DIFFRACTION100
2.7157-2.80330.31161390.25934832X-RAY DIFFRACTION100
2.8033-2.90350.26891450.25474837X-RAY DIFFRACTION100
2.9035-3.01970.2941410.25654842X-RAY DIFFRACTION100
3.0197-3.1570.29831410.24834827X-RAY DIFFRACTION100
3.157-3.32340.22811420.22984887X-RAY DIFFRACTION100
3.3234-3.53150.26021410.2234855X-RAY DIFFRACTION100
3.5315-3.8040.21061440.20284875X-RAY DIFFRACTION100
3.804-4.18640.1881420.19384865X-RAY DIFFRACTION100
4.1864-4.79120.19911460.17644919X-RAY DIFFRACTION100
4.7912-6.03290.23291430.20934957X-RAY DIFFRACTION100
6.0329-39.14110.20731530.20335051X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 69.2837 Å / Origin y: -13.827 Å / Origin z: -1.6677 Å
111213212223313233
T0.577 Å2-0.1519 Å20.0129 Å2-0.4613 Å20.0027 Å2--0.6928 Å2
L0.7677 °20.6995 °20.4513 °2-1.5642 °20.1812 °2--0.4155 °2
S-0.1456 Å °0.1585 Å °0.0248 Å °-0.2286 Å °0.1739 Å °0.0524 Å °0.0353 Å °-0.0322 Å °-0.03 Å °
Refinement TLS groupSelection details: all

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