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- PDB-4ogx: Crystal structure of Fab DX-2930 in complex with human plasma kal... -

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Basic information

Entry
Database: PDB / ID: 4ogx
TitleCrystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom resolution
Components
  • DX-2930 HEAVY CHAIN
  • DX-2930 LIGHT CHAIN
  • Plasma kallikrein
KeywordsHYDROLASE/ANTIBODY / FAB / ANTIBODY / KALLIKREIN / BLOOD / PLASMA / PLASMA KALLIKREIN- MEDIATED EDEMA / ACUTE HEREDITARY ANGIOEDEMA / HAE / HMWK / serpin C1-inhibitor / C1-INH / hereditary angioedema / HAW / bradykinin / Fletcher factor / Kininogenin / serine protease / edema / HYDROLASE-ANTIBODY complex
Function / homology
Function and homology information


plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / immunoglobulin complex / fibrinolysis ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / immunoglobulin complex / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / adaptive immune response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Trypsin-like serine proteases / Thrombin, subunit H / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Plasma kallikrein / Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsEdwards, T.E. / Clifton, M.C. / Abendroth, J. / Nixon, A. / Ladner, R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Inhibition of plasma kallikrein by a highly specific active site blocking antibody.
Authors: Kenniston, J.A. / Faucette, R.R. / Martik, D. / Comeau, S.R. / Lindberg, A.P. / Kopacz, K.J. / Conley, G.P. / Chen, J. / Viswanathan, M. / Kastrapeli, N. / Cosic, J. / Mason, S. / DiLeo, M. ...Authors: Kenniston, J.A. / Faucette, R.R. / Martik, D. / Comeau, S.R. / Lindberg, A.P. / Kopacz, K.J. / Conley, G.P. / Chen, J. / Viswanathan, M. / Kastrapeli, N. / Cosic, J. / Mason, S. / DiLeo, M. / Abendroth, J. / Kuzmic, P. / Ladner, R.C. / Edwards, T.E. / TenHoor, C. / Adelman, B.A. / Nixon, A.E. / Sexton, D.J.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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: Plasma kallikrein
H: DX-2930 HEAVY CHAIN
L: DX-2930 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2069
Polymers74,6303
Non-polymers5766
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-30 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.610, 171.500, 42.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Plasma kallikrein / Fletcher factor / Kininogenin / Plasma prekallikrein / Plasma kallikrein heavy chain / Plasma ...Fletcher factor / Kininogenin / Plasma prekallikrein / Plasma kallikrein heavy chain / Plasma kallikrein light chain


Mass: 27144.842 Da / Num. of mol.: 1 / Fragment: UNP residues 391-631 / Mutation: N396E, N453E, N494E, C503S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK3, KLKB1, KLKB1_HUMAN / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03952, plasma kallikrein
#2: Antibody DX-2930 HEAVY CHAIN


Mass: 24039.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: S6C4R2*PLUS
#3: Antibody DX-2930 LIGHT CHAIN


Mass: 23446.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Y4*PLUS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST WIZ3-4 screen condition H7, 30% MPD, 10% PEG 3350, 0.1 M imidazole pH 6.5, 0.2 M ammonium sulfate, unique ...Details: FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST WIZ3-4 screen condition H7, 30% MPD, 10% PEG 3350, 0.1 M imidazole pH 6.5, 0.2 M ammonium sulfate, unique puck ID QJO1-12, crystal tracking ID 242118H7 , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 21, 2013 / Details: VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 32254 / Num. obs: 32218 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 30.87 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.74
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 2422 / Num. unique obs: 426 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANY

2any


Resolution: 2.4→41.12 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.883 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1598 5 %RANDOM
Rwork0.185 ---
obs0.188 32165 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.45 Å2 / Biso mean: 25.07 Å2 / Biso min: 3.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0 Å20 Å2
2--0.17 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 30 270 5334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195192
X-RAY DIFFRACTIONr_bond_other_d0.0010.024706
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9467086
X-RAY DIFFRACTIONr_angle_other_deg0.7863.00310817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96724.195205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74515795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1811521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5722.5292653
X-RAY DIFFRACTIONr_mcbond_other1.5732.5282652
X-RAY DIFFRACTIONr_mcangle_it2.5473.7843311
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 108 -
Rwork0.241 2199 -
all-2307 -
obs--99.35 %

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