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- PDB-6q9i: Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6q9i
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Factor X peptide fragment (39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor XFactor 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 / 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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / 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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis / coagulation factor Xa / pattern specification process / positive regulation of intracellular protein transport / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / activation of cysteine-type endopeptidase activity / face morphogenesis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / structural constituent of muscle / positive regulation of calcium ion transport into cytosol / response to ATP / 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 / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / Intrinsic Pathway of Fibrin Clot Formation / muscle contraction / calcium ion transmembrane transport / phospholipid binding / regulation of protein stability / Stimuli-sensing channels / Golgi lumen / blood coagulation / cell population proliferation / transmembrane transporter binding / electron transfer activity / positive regulation of cell migration / negative regulation of cell population proliferation / external side of plasma membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / 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 / Coagulation factor-like, Gla domain superfamily ...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-type aspartate/asparagine hydroxylation site / EGF-like domain / 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. / TPR repeat profile. / Epidermal growth factor-like domain. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Tetratricopeptide-like helical domain superfamily / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 Å
AuthorsChowdhury, R. / Pfeffer, I. / Schofield, C.J.
CitationJournal: To Be Published
Title: AspH-H679A.Factor X Complex
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)53,8517
Polymers53,5292
Non-polymers3225
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-6 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.125, 91.359, 123.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Coagulation factor X / 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
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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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: 7.5 / Details: 0.2 M sodium formate, 20 % w/v PEG 3350

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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: 1.85→46.447 Å / Num. obs: 49046 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.027 / Rrim(I) all: 0.081 / Net I/σ(I): 27.09
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4787 / CC1/2: 0.705 / Rpim(I) all: 0.457 / % 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: 6Q9F

6q9f


Resolution: 1.852→46.447 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.2233 2451 5.01 %
Rwork0.202 --
obs0.2031 48960 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 52.2 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 59 Å2
Refinement stepCycle: LAST / Resolution: 1.852→46.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 21 330 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073728
X-RAY DIFFRACTIONf_angle_d0.9735041
X-RAY DIFFRACTIONf_dihedral_angle_d16.032240
X-RAY DIFFRACTIONf_chiral_restr0.05528
X-RAY DIFFRACTIONf_plane_restr0.006661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8524-1.88810.33971250.33672440X-RAY DIFFRACTION97
1.8881-1.92660.33091470.30652557X-RAY DIFFRACTION100
1.9266-1.96850.33851400.28322538X-RAY DIFFRACTION100
1.9685-2.01430.25311320.26252559X-RAY DIFFRACTION100
2.0143-2.06470.28851320.25782546X-RAY DIFFRACTION100
2.0647-2.12050.29631340.24822570X-RAY DIFFRACTION100
2.1205-2.18290.29541260.24082593X-RAY DIFFRACTION100
2.1829-2.25330.26351000.23422574X-RAY DIFFRACTION100
2.2533-2.33390.24961380.23082564X-RAY DIFFRACTION100
2.3339-2.42730.25711430.22852566X-RAY DIFFRACTION100
2.4273-2.53780.23351370.21452580X-RAY DIFFRACTION100
2.5378-2.67160.22971330.21112585X-RAY DIFFRACTION100
2.6716-2.83890.23091480.21622588X-RAY DIFFRACTION100
2.8389-3.05810.24211490.212581X-RAY DIFFRACTION100
3.0581-3.36570.23291490.20782600X-RAY DIFFRACTION100
3.3657-3.85260.21781330.17942637X-RAY DIFFRACTION100
3.8526-4.8530.16041460.15552638X-RAY DIFFRACTION100
4.853-46.46190.19691390.18532793X-RAY DIFFRACTION99
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)
13.6296-0.0694-0.36792.85250.35633.33290.24630.74750.1631-0.5186-0.24470.81050.117-0.34640.00590.43930.1235-0.06280.4686-0.10770.673756.2983.7218-6.2064
23.37181.0541.75832.25360.36043.24250.9517-0.60870.39320.6526-0.65840.56940.4967-0.58-0.18630.598-0.17750.10520.3706-0.16960.563259.59085.30767.9198
30.6553-0.65530.13581.79651.40814.94660.34760.12110.0408-0.48340.426-0.5898-0.83570.5223-0.52090.6076-0.24460.26030.4156-0.11870.543771.838324.002122.5595
43.22350.1013-3.0652.5211.11126.49830.19380.42230.1221-0.2954-0.0403-0.0055-0.7297-0.971-0.05210.1910.1375-0.0210.28210.02120.21153.190525.099646.635
50.2728-0.35540.55691.95321.34386.4884-0.1950.7171-0.6307-0.5209-0.10140.15960.6513-0.3730.20560.4559-0.02730.08390.4877-0.12270.438659.880816.963330.9345
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 553 )
4X-RAY DIFFRACTION4chain 'A' and (resid 554 through 758 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 116 )

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