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

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Basic information

Entry
Database: PDB / ID: 4ogy
TitleCrystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 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 / immunoglobulin complex / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / immunoglobulin complex / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / adaptive immune response / 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 / Immunoglobulin V-set domain / Serine proteases, trypsin family, histidine active site ...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 / 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 / Trypsin-like serine proteases / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Thrombin, subunit H / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / 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: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasma kallikrein
B: Plasma kallikrein
H: DX-2930 HEAVY CHAIN
L: DX-2930 LIGHT CHAIN
M: DX-2930 HEAVY CHAIN
N: DX-2930 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,4469
Polymers149,2606
Non-polymers1863
Water18,3751020
1
A: Plasma kallikrein
H: DX-2930 HEAVY CHAIN
L: DX-2930 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8166
Polymers74,6303
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasma kallikrein
M: DX-2930 HEAVY CHAIN
N: DX-2930 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)74,6303
Polymers74,6303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.120, 113.760, 89.050
Angle α, β, γ (deg.)90.000, 94.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 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.: 2 / 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03952, plasma kallikrein
#2: Antibody DX-2930 HEAVY CHAIN


Mass: 24039.129 Da / Num. of mol.: 2
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.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 2.8 Å3/Da / Density % sol: 56 %
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 INDEX screen condition D10, 20% PEG 5000 MME, 0.1 M BisTris pH 6.5 supplemented with 20% ethylene glycol as ...Details: FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST INDEX screen condition D10, 20% PEG 5000 MME, 0.1 M BisTris pH 6.5 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID qjo1-15, crystal tracking ID 242121d10, 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 22, 2013 / Details: VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 95084 / Num. obs: 94897 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 28.24 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5.8 / Num. measured obs: 7650 / Num. unique obs: 1098 / % possible all: 98.8

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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
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANY AND 3IDX

2any

3idx


Resolution: 2.1→40.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.417 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4757 5 %RANDOM
Rwork0.183 ---
obs0.185 94873 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.74 Å2 / Biso mean: 26.51 Å2 / Biso min: 6.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.07 Å2
2---0.15 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9991 0 12 1020 11023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910321
X-RAY DIFFRACTIONr_bond_other_d0.0040.029394
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.94214082
X-RAY DIFFRACTIONr_angle_other_deg0.9543.00321610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55351331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17824.358413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.144151593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.851541
X-RAY DIFFRACTIONr_chiral_restr0.0830.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111819
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022358
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_it0.8070.9545294
X-RAY DIFFRACTIONr_mcbond_other0.8070.9545293
X-RAY DIFFRACTIONr_mcangle_it1.4411.4216605
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: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 366 -
Rwork0.202 6549 -
all-6915 -
obs--98.8 %
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)
10.857-0.11790.13550.8735-0.21320.9038-0.00360.01970.08710.00940.03140.01160.0354-0.0087-0.02780.0815-0.009-0.00110.130.02270.1585-6.1938-6.008722.2436
21.31580.1332-0.22160.6458-0.13740.4159-0.0397-0.0196-0.1390.00460.02020.0027-0.0183-0.00470.01950.0853-0.00680.00240.14260.01070.1815-47.3336-5.255819.1552
30.47560.1019-0.01290.62690.15120.0605-0.0120.1128-0.0271-0.0610.0236-0.1221-0.0032-0.0592-0.01150.2179-0.0260.03250.1819-0.03120.08035.4564-49.408314.2384
40.14190.1172-0.01121.0501-0.22740.1716-0.08210.0436-0.04280.07220.0783-0.10790.0056-0.00350.00390.19610.01590.00670.1278-0.02160.14598.2385-54.468431.3882
50.1004-0.0872-0.30780.10530.36751.54730.1359-0.0088-0.0016-0.0583-0.0331-0.0465-0.2694-0.3751-0.10290.3037-0.0425-0.08430.29180.04260.0881-34.837435.647932.5956
60.03920.191-0.09141.5692-0.920.96040.02590.0161-0.04690.33210.0209-0.0562-0.3541-0.1235-0.04680.26590.0189-0.00280.13910.01850.1305-32.356842.712615.1356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A391 - 629
2X-RAY DIFFRACTION2B391 - 629
3X-RAY DIFFRACTION3H1 - 223
4X-RAY DIFFRACTION4L1 - 212
5X-RAY DIFFRACTION5M2 - 222
6X-RAY DIFFRACTION6N1 - 212

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