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- PDB-6q9f: Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6q9f
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor X
KeywordsGENE REGULATION / OXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / 2-OXOGLUTARATE DEPENDENT OXYGENASE / OXYGENASE / HYPOXIA / METAL-BINDING / TRANSCRIPTION / ASPARTYL/ASPARAGINYL BETA-2 HYDROXYLASE / ASPH / EGF-LIKE DOMAIN HYDROXYLASE / DOUBLE STRANDED BETA-HELIX / FACIAL TRIAD / CYTOPLASM / TPR / TETRATRICOPEPTIDE REPEAT / BETA-HYDROXYLATION / SIGNALING / DEVELOPMENT / VITAMIN C
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / peptidyl-aspartic acid hydroxylation / 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 / limb morphogenesis ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / peptidyl-aspartic acid hydroxylation / 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 / limb morphogenesis / cortical endoplasmic reticulum / pattern specification process / coagulation factor Xa / positive regulation of intracellular protein transport / : / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / face morphogenesis / Extrinsic Pathway of Fibrin Clot Formation / structural constituent of muscle / response to ATP / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / positive regulation of TOR signaling / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / regulation of ryanodine-sensitive calcium-release channel activity / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / muscle contraction / calcium channel complex / Intrinsic Pathway of Fibrin Clot Formation / sarcoplasmic reticulum membrane / cellular response to calcium ion / regulation of protein stability / Stimuli-sensing channels / phospholipid binding / calcium ion transmembrane transport / Golgi lumen / blood coagulation / transmembrane transporter binding / cell population proliferation / electron transfer activity / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / negative regulation of cell population proliferation / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : ...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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / TPR repeat region circular profile. / Epidermal growth factor-like domain. / TPR repeat profile. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsChowdhury, R. / Pfeffer, I. / Schofield, C.J.
CitationJournal: To Be Published
Title: Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser)
Authors: Pfeffer, I. / Chowdhury, R. / Schofield, C.J.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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
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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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
Revision 1.2Oct 9, 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: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0077
Polymers53,5292
Non-polymers4785
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-15 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.808, 91.541, 122.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 49338.270 Da / Num. of mol.: 1 / Mutation: H679A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Plasmid: PET-28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 4190.384 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa

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Non-polymers , 4 types, 399 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium chloride 0.1 M Tris-HCl 8.0 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2014 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.63→46.161 Å / Num. obs: 70950 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.02 / Rrim(I) all: 0.064 / Net I/σ(I): 35.59
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 13 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.875 / Num. unique obs: 6975 / CC1/2: 0.891 / Rpim(I) all: 0.453 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQY

5jqy


Resolution: 1.63→46.161 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.46
RfactorNum. reflection% reflection
Rfree0.1999 3465 4.89 %
Rwork0.1812 --
obs0.1822 70858 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 49.3 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 1.63→46.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 29 394 4010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123893
X-RAY DIFFRACTIONf_angle_d1.1995276
X-RAY DIFFRACTIONf_dihedral_angle_d7.4883193
X-RAY DIFFRACTIONf_chiral_restr0.059546
X-RAY DIFFRACTIONf_plane_restr0.009698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6304-1.65270.31951310.29782645X-RAY DIFFRACTION99
1.6527-1.67630.30911240.28452655X-RAY DIFFRACTION100
1.6763-1.70130.26691450.25812657X-RAY DIFFRACTION100
1.7013-1.72790.25931310.24812683X-RAY DIFFRACTION100
1.7279-1.75630.281380.24732650X-RAY DIFFRACTION100
1.7563-1.78650.26771410.24092675X-RAY DIFFRACTION100
1.7865-1.8190.24931700.22042594X-RAY DIFFRACTION100
1.819-1.8540.2751420.2172692X-RAY DIFFRACTION100
1.854-1.89190.25191510.20772650X-RAY DIFFRACTION100
1.8919-1.9330.22991240.20732685X-RAY DIFFRACTION100
1.933-1.9780.21661120.19132693X-RAY DIFFRACTION100
1.978-2.02740.22831270.19492674X-RAY DIFFRACTION100
2.0274-2.08230.24061220.19082737X-RAY DIFFRACTION100
2.0823-2.14350.19481390.18372630X-RAY DIFFRACTION100
2.1435-2.21270.18691530.18292690X-RAY DIFFRACTION100
2.2127-2.29180.19151330.18242696X-RAY DIFFRACTION100
2.2918-2.38360.22471470.17872685X-RAY DIFFRACTION100
2.3836-2.4920.19671280.17692711X-RAY DIFFRACTION100
2.492-2.62340.20311410.17572709X-RAY DIFFRACTION100
2.6234-2.78770.19691500.18142703X-RAY DIFFRACTION100
2.7877-3.0030.22071350.18112707X-RAY DIFFRACTION100
3.003-3.30510.21181560.18642716X-RAY DIFFRACTION100
3.3051-3.78310.15851430.16762745X-RAY DIFFRACTION100
3.7831-4.76560.17211490.14662783X-RAY DIFFRACTION100
4.7656-46.17970.19141330.18292928X-RAY DIFFRACTION100
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)
12.3611-0.0775-0.3080.98460.27871.52520.07190.54340.291-0.2831-0.08610.60160.0016-0.349-0.02260.45110.097-0.08270.3915-0.00610.580256.01263.7099-6.8696
21.2287-0.13310.76090.50210.0160.6010.4671-0.37210.36570.3503-0.45060.42750.2567-0.2932-0.02690.5692-0.12630.08070.3634-0.1560.563957.89976.15767.2482
30.4598-0.67940.00911.00650.46642.08930.16080.02590.0723-0.18590.2816-0.3748-0.08590.1719-0.36710.4386-0.17370.15130.3686-0.11730.464872.518922.265721.4583
42.34690.2818-2.1071.1717-0.00513.7320.09630.37040.1964-0.16560.1031-0.0202-0.3588-0.6279-0.11160.19860.07140.00030.24030.03710.194853.474626.30145.1694
50.8131-0.0572-0.26631.44620.32221.7179-0.26160.3163-0.342-0.30410.1570.06020.8497-0.27030.15530.5346-0.10690.08530.4701-0.0580.408259.649217.239930.3912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 374 )
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 433 )
3X-RAY DIFFRACTION3chain 'A' and (resid 434 through 538 )
4X-RAY DIFFRACTION4chain 'A' and (resid 539 through 758 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 116 )

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