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- PDB-6l63: Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic ... -

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Basic information

Entry
Database: PDB / ID: 6l63
TitleHuman Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3 containing two (1S,2S)-2-ACHC residues
Components
  • Coagulation factor XII
  • F3
KeywordsBLOOD CLOTTING / Enzyme
Function / homology
Function and homology information


coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / misfolded protein binding / positive regulation of fibrinolysis / zymogen activation ...coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / misfolded protein binding / positive regulation of fibrinolysis / zymogen activation / Defective factor XII causes hereditary angioedema / protein autoprocessing / positive regulation of blood coagulation / rough endoplasmic reticulum / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / protein processing / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
triacetyl-beta-chitotriose / ACETYL GROUP / Coagulation factor XII
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSengoku, T. / Katoh, T. / Hirata, K. / Suga, H. / Ogata, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and Technology Japan
Japan Society for the Promotion of Science Japan
CitationJournal: Nat.Chem. / Year: 2020
Title: Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic beta-amino acids.
Authors: Katoh, T. / Sengoku, T. / Hirata, K. / Ogata, K. / Suga, H.
History
DepositionOct 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XII
B: F3
C: Coagulation factor XII
D: F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9268
Polymers56,7864
Non-polymers1,1404
Water00
1
A: Coagulation factor XII
B: F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8614
Polymers28,3932
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint8 kcal/mol
Surface area11010 Å2
MethodPISA
2
C: Coagulation factor XII
D: F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0654
Polymers28,3932
Non-polymers6722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint10 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.260, 105.520, 123.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 373 through 420 or (resid 421...
21(chain C and (resid 373 through 433 or resid 435...
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 373 through 420 or (resid 421...A373 - 420
121(chain A and (resid 373 through 420 or (resid 421...A421
211(chain C and (resid 373 through 433 or resid 435...C373 - 433
221(chain C and (resid 373 through 433 or resid 435...C435 - 490
231(chain C and (resid 373 through 433 or resid 435...C500 - 525
241(chain C and (resid 373 through 433 or resid 435...C527 - 569
251(chain C and (resid 373 through 433 or resid 435...C578 - 615
112chain BB1 - 19
212chain DD1 - 19

NCS ensembles :
ID
1
2

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Components

#1: Protein Coagulation factor XII / Hageman factor / HAF


Mass: 26127.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00748, coagulation factor XIIa
#2: Protein/peptide F3


Mass: 2265.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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.: 1
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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.89 Å3/Da / Density % sol: 68.37 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris pH 6.0~6.5, 24~26% PEG3350, and 200 mM NaCl or 200 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→14.963 Å / Num. obs: 18309 / % possible obs: 98.93 % / Redundancy: 44.5 % / CC1/2: 0.966 / Net I/σ(I): 6.23
Reflection shellResolution: 3→3.106 Å / Num. unique obs: 1809 / CC1/2: 0.721

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3546refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B77

6b77


Resolution: 3→14.963 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3024 1708 9.33 %
Rwork0.2579 16591 -
obs0.262 18299 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.58 Å2 / Biso mean: 37.7119 Å2 / Biso min: 7.36 Å2
Refinement stepCycle: final / Resolution: 3→14.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 70 0 3797
Biso mean--44.9 --
Num. residues----495
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1649X-RAY DIFFRACTIONPOSITIONAL0.089
12C1649X-RAY DIFFRACTIONPOSITIONAL0.089
21B162X-RAY DIFFRACTIONPOSITIONAL0.074
22D162X-RAY DIFFRACTIONPOSITIONAL0.074
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0002-3.08770.42011450.35551360
3.0877-3.18650.36451430.31181347
3.1865-3.29920.33771350.29551368
3.2992-3.42970.31991420.27731365
3.4297-3.58380.29871370.23781363
3.5838-3.76990.28111430.24061367
3.7699-4.00180.28151410.22241376
4.0018-4.3040.2521410.21591376
4.304-4.72470.24441400.22471379
4.7247-5.38040.29131440.23991401
5.3804-6.67690.30741450.27491417
6.6769-14.9630.32011520.28411472

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