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- PDB-2w2q: PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR -

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Basic information

Entry
Database: PDB / ID: 2w2q
TitlePCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR
Components
  • (PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9) x 2
  • LOW-DENSITY LIPOPROTEIN RECEPTOR
KeywordsHYDROLASE/RECEPTOR / HYDROLASE-RECEPTOR COMPLEX / PCSK9 / LDLR / PROPROTEIN CONVERTASE / LOW-DENSITY LIPOPROTEIN RECEPTOR / EGF / CARDIOVASCULAR DISEASE / FAMILIAL HYPERCHOLESTEROLEMIA / LIPID METABOLISM / SERINE PROTEASE / HYDROLASE / LIPID TRANSPORT / STEROID METABOLISM / RECEPTOR
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / negative regulation of astrocyte activation / positive regulation of lysosomal protein catabolic process / low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / negative regulation of astrocyte activation / positive regulation of lysosomal protein catabolic process / low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / PCSK9-AnxA2 complex / positive regulation of triglyceride biosynthetic process / negative regulation of receptor recycling / intestinal cholesterol absorption / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / clathrin heavy chain binding / Chylomicron clearance / low-density lipoprotein particle receptor activity / amyloid-beta clearance by cellular catabolic process / positive regulation of low-density lipoprotein particle receptor catabolic process / low-density lipoprotein particle binding / LDL clearance / high-density lipoprotein particle clearance / lipoprotein catabolic process / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / transporter inhibitor activity / phospholipid transport / cholesterol transport / signaling receptor inhibitor activity / low-density lipoprotein particle / negative regulation of receptor internalization / COPII-coated ER to Golgi transport vesicle / response to caloric restriction / negative regulation of amyloid fibril formation / sodium channel inhibitor activity / cellular response to fatty acid / endolysosome membrane / negative regulation of low-density lipoprotein particle clearance / negative regulation of protein metabolic process / artery morphogenesis / regulation of cholesterol metabolic process / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / sorting endosome / protein autoprocessing / lipoprotein particle binding / amyloid-beta clearance / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of receptor internalization / apolipoprotein binding / cellular response to low-density lipoprotein particle stimulus / retinoid metabolic process / cholesterol metabolic process / Retinoid metabolism and transport / long-term memory / phagocytosis / phospholipid metabolic process / clathrin-coated pit / somatodendritic compartment / neurogenesis / receptor-mediated endocytosis / regulation of neuron apoptotic process / cholesterol homeostasis / cellular response to starvation / VLDLR internalisation and degradation / Post-translational protein phosphorylation / lipid metabolic process / kidney development / liver development / clathrin-coated endocytic vesicle membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron differentiation / cellular response to insulin stimulus / endocytosis / apical part of cell / positive regulation of inflammatory response / late endosome / positive regulation of neuron apoptotic process / Cargo recognition for clathrin-mediated endocytosis / amyloid-beta binding / Clathrin-mediated endocytosis / virus receptor activity / protease binding / endopeptidase activity / molecular adaptor activity / basolateral plasma membrane / early endosome / lysosome / signaling receptor complex / endosome membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity
Similarity search - Function
Peptidase S8 propeptide/proteinase inhibitor I9 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B ...Peptidase S8 propeptide/proteinase inhibitor I9 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Proteinase K-like catalytic domain / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Laminin / Laminin / : / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 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 / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsBottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. ...Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Biochemical Characterization of the Wild Type Pcsk9/Egf-Ab Complex and Natural Fh Mutants.
Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. ...Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A.
History
DepositionNov 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
E: LOW-DENSITY LIPOPROTEIN RECEPTOR
P: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9865
Polymers57,9063
Non-polymers802
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-27.1 kcal/mol
Surface area22100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)88.370, 88.370, 218.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 / PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED ...PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1


Mass: 33131.285 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 153-451 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein LOW-DENSITY LIPOPROTEIN RECEPTOR / LDL RECEPTOR


Mass: 12095.453 Da / Num. of mol.: 1 / Fragment: EGF-A DOMAIN, RESIDUES 314-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01130
#3: Protein PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 / PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED ...PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1


Mass: 12679.604 Da / Num. of mol.: 1 / Fragment: PROPEPTIDE, RESIDUES 53-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NBP7
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 374 TO HIS
Has protein modificationY
Sequence detailsHUMAN PCSK9 PRODOMAIN. THE FIRST 14 RESIDUES IN THE SEQUENCE ARE A RESULT OF THE CLONING PROCEDURE. ...HUMAN PCSK9 PRODOMAIN. THE FIRST 14 RESIDUES IN THE SEQUENCE ARE A RESULT OF THE CLONING PROCEDURE. THE 15TH RESIDUE CORRESPONDS TO ALA53 OF WT PCSK9 HUMAN LDLR EGF-AB DOMAINS. THE FIRST 27 RESIDUES IN THE SEQUENCE ARE A 6HIS TAG AND A LINKER FROM THE CLONING PROCEDURE. THE 28TH RESIDUE CORRESPONDS TO GLY293 OF WT LDLR HUMAN PCSK9 CATALYTIC DOMAIN. THE LAST 13 RESIDUES ARE A LINKER AND A 6HIS TAG, RESULTING FROM THE CLONING PROCEDURE. THE FIRST RESIDUE CORRESPONDS TO SER153 OF WT PCSK9.

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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: 4.02 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.33→40 Å / Num. obs: 37593 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.1
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTW

2qtw


Resolution: 2.33→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.491 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25279 1872 5 %RANDOM
Rwork0.21932 ---
obs0.22095 35652 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.689 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2--1.79 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.33→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 2 195 3326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223243
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9674415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00523.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25815530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3141525
X-RAY DIFFRACTIONr_chiral_restr0.0760.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022457
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.21438
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22168
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4751.52127
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87123345
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.99431225
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7074.51064
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 128
Rwork0.302 2599
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)
11.08650.0081-0.42290.9599-0.52062.07060.0845-0.1333-0.07630.0915-0.103-0.0444-0.38550.08650.01850.012-0.0392-0.01550.17050.02760.0026-17.534-4.811929.7306
21.6947-1.1428-1.54961.90881.0473.74520.07010.0526-0.24110.0181-0.11030.0766-0.08090.07590.0402-0.08840.0042-0.02780.17890.04690.0852-2.2835-17.66889.5314
30.72160.0188-0.74810.6658-0.70613.88750.12880.00230.00330.1669-0.14060.0284-0.34610.24140.01170.0105-0.05840.02230.20780.02770.0296-32.4374-16.086352.1126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A153 - 447
2X-RAY DIFFRACTION2E285 - 332
3X-RAY DIFFRACTION3P60 - 152

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