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- PDB-6rk9: Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR dom... -

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Basic information

Entry
Database: PDB / ID: 6rk9
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X
Components
  • ACA-LYS-ASP-GLY-LEU-GLY-GLU-TYR-THR-CYS-THR-SER-LEU-GLU-GLY-PHE-GLU
  • Aspartyl/asparaginyl beta-hydroxylase
KeywordsOXIDOREDUCTASE / 2-oxoglutarate dependent oxygenase / aspartyl/asparaginyl beta-hydroxylase / EGF-like domain hydroxylase / double stranded beta-helix / tetratricopeptide repeat
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / cortical endoplasmic reticulum / limb morphogenesis ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / cortical endoplasmic reticulum / limb morphogenesis / positive regulation of intracellular protein transport / pattern specification process / face morphogenesis / structural constituent of muscle / response to ATP / Protein hydroxylation / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of proteolysis / detection of calcium ion / regulation of cytosolic calcium ion concentration / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium channel complex / muscle contraction / sarcoplasmic reticulum membrane / cellular response to calcium ion / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / transmembrane transporter binding / electron transfer activity / cell population proliferation / negative regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / plasma membrane
Similarity search - Function
Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.292 Å
AuthorsMcDonough, M.A. / Pfeffer, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Aspartate/asparagine-beta-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern.
Authors: Pfeffer, I. / Brewitz, L. / Krojer, T. / Jensen, S.A. / Kochan, G.T. / Kershaw, N.J. / Hewitson, K.S. / McNeill, L.A. / Kramer, H. / Munzel, M. / Hopkinson, R.J. / Oppermann, U. / Handford, ...Authors: Pfeffer, I. / Brewitz, L. / Krojer, T. / Jensen, S.A. / Kochan, G.T. / Kershaw, N.J. / Hewitson, K.S. / McNeill, L.A. / Kramer, H. / Munzel, M. / Hopkinson, R.J. / Oppermann, U. / Handford, P.A. / McDonough, M.A. / Schofield, C.J.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionMay 8, 2019ID: 5JZZ
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Aspartyl/asparaginyl beta-hydroxylase
C: ACA-LYS-ASP-GLY-LEU-GLY-GLU-TYR-THR-CYS-THR-SER-LEU-GLU-GLY-PHE-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2227
Polymers100,8183
Non-polymers4044
Water4,143230
1
A: Aspartyl/asparaginyl beta-hydroxylase
C: ACA-LYS-ASP-GLY-LEU-GLY-GLU-TYR-THR-CYS-THR-SER-LEU-GLU-GLY-PHE-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6154
Polymers51,4132
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-16 kcal/mol
Surface area19680 Å2
MethodPISA
2
B: Aspartyl/asparaginyl beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,4051
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-8 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.472, 59.243, 95.665
Angle α, β, γ (deg.)103.970, 91.490, 92.700
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aspartyl/asparaginyl beta-hydroxylase / Aspartate beta-hydroxylase / ASP beta-hydroxylase / Peptide-aspartate beta-dioxygenase


Mass: 49405.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide ACA-LYS-ASP-GLY-LEU-GLY-GLU-TYR-THR-CYS-THR-SER-LEU-GLU-GLY-PHE-GLU


Mass: 2007.180 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The ACA residue is an artificial linker within this synthetic cyclic peptide.
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-tris propane, 200 mM potassium thiocyanate, 20% PEG 3350, 2 mM N-oxalylglycine, 1 mM manganese chloride, 3.3 mM cyclic peptide, 18 mg/ml asph protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 4, 2014 / Details: OSMIC HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.292→50 Å / Num. obs: 46948 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.069 / Rrim(I) all: 0.145 / Χ2: 1.058 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.292-2.385.50.99247430.6710.4661.057100
2.38-2.485.50.95647260.7620.4481.079100
2.48-2.595.50.82146750.8020.3821.0881000.907
2.59-2.735.60.6647010.8760.3071.0861000.729
2.73-2.95.60.47246850.9280.2181.0911000.52
2.9-3.125.70.30546950.9610.1411.0421000.336
3.12-3.445.70.16746710.980.0770.94999.90.184
3.44-3.935.80.10246840.990.0471.03899.90.112
3.93-4.955.70.08147180.9940.0371.0899.80.09
4.95-505.80.06146500.9970.0281.07199.60.067

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQY

5jqy


Resolution: 2.292→31.997 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.24
RfactorNum. reflection% reflection
Rfree0.235 1965 4.19 %
Rwork0.2107 --
obs0.2117 46871 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 54.2343 Å2 / Biso min: 23.54 Å2
Refinement stepCycle: final / Resolution: 2.292→31.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6966 0 22 230 7218
Biso mean--42.75 45.35 -
Num. residues----875
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2922-2.34950.32261320.30583005313792
2.3495-2.4130.32311420.290532003342100
2.413-2.4840.30251440.280632723416100
2.484-2.56410.30681390.284232143353100
2.5641-2.65570.28381430.27732043347100
2.6557-2.7620.28011460.283232353381100
2.762-2.88770.32041460.269832413387100
2.8877-3.03980.31031340.24832043338100
3.0398-3.23010.25721380.245532283366100
3.2301-3.47920.22631370.211132223359100
3.4792-3.82880.22391460.183432473393100
3.8288-4.38160.18631390.17473188332799
4.3816-5.51580.1841420.16583214335699
5.5158-32.00030.1931370.167132323369100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9540.91420.24180.43280.21740.73280.2280.26940.12030.1186-0.13030.0522-0.0771-0.172300.48320.09540.10320.44880.02330.416154.290510.3881-74.8775
20.0996-0.10960.4040.1433-0.42670.68630.09680.03330.1222-0.1201-0.1103-0.1179-0.34030.7115-00.5289-0.18790.02390.62970.03350.456569.536214.0136-48.0053
31.43560.333-0.29711.0833-0.29471.215-0.04880.12920.0423-0.02760.14360.1191-0.1193-0.087300.2618-0.0055-0.02770.32-0.01650.254651.48312.9236-26.2717
40.35050.26850.2090.186-0.21811.22640.1297-0.06640.02170.0759-0.2044-0.03060.24810.2235-00.5910.06460.01420.33580.04560.569546.407-20.4195-67.4016
50.979-0.4354-0.46511.10850.07841.0374-0.0263-0.08660.01890.14810.01080.04710.03340.029600.2737-0.0119-0.03020.30810.00220.253227.38094.9321-96.3075
60.0020.0042-0.01170.005-0.00850.00260.20270.1970.0735-0.2092-0.1245-0.0479-0.0432-0.0709-00.5329-0.2130.02550.72850.15580.471957.97245.1576-33.898
70.00530.01720.02080.04520.02660.01230.49310.01-0.17010.0743-0.0512-0.10660.4125-0.0607-00.6485-0.14470.10110.8070.03310.46253.7455.186-49.3669
80.2158-0.0730.23131.0925-0.21470.17250.05630.0942-0.00010.10040.0119-0.04690.06130.0211-00.26750.0110.01630.3118-0.00210.303929.7153-1.4302-100.0299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 433)A330 - 433
2X-RAY DIFFRACTION2chain 'A' and (resid 434 through 538 )A434 - 538
3X-RAY DIFFRACTION3chain 'A' and (resid 539 through 758 )A539 - 758
4X-RAY DIFFRACTION4chain 'B' and (resid 330 through 556 )B330 - 556
5X-RAY DIFFRACTION5chain 'B' and (resid 557 through 663 )B557 - 663
6X-RAY DIFFRACTION6chain 'C' and (resid 254 through 258 )C254 - 258
7X-RAY DIFFRACTION7chain 'C' and (resid 259 through 269 )C259 - 269
8X-RAY DIFFRACTION8chain 'B' and (resid 664 through 758)B664 - 758

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