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- PDB-4cdd: Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophen... -

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Basic information

Entry
Database: PDB / ID: 4cdd
TitleHuman DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophenyl) phenyl)ethyl)piperidine-2-carboxamide
Components(DIPEPTIDYL PEPTIDASE 1 ...) x 3
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / phosphatase binding / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / : / lysosome / immune response / endoplasmic reticulum lumen / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Lipocalin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-GDI / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDebreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. ...Debreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Cage, P. / Sanghanee, H. / Breed, J. / Wissler, L.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Cathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate.
Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / ...Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / Chohan, K. / Beri, R. / Thong, B. / Wallace, A. / Oreffo, V. / Hutchinson, R. / Harper, S. / Debreczeni, J. / Breed, J. / Wissler, L. / Edman, K.
History
DepositionOct 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,50914
Polymers79,6296
Non-polymers1,8808
Water1,69394
1
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4326
Polymers39,8153
Non-polymers6173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-66.5 kcal/mol
Surface area14960 Å2
MethodPISA
2
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0778
Polymers39,8153
Non-polymers1,2635
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-55.8 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.291, 84.291, 221.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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DIPEPTIDYL PEPTIDASE 1 ... , 3 types, 6 molecules ADBECF

#1: Protein DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN / DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I ...DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 13601.268 Da / Num. of mol.: 2 / Fragment: DPP1 EXCLUSION DOMAIN, RESIDUES 25-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN / DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 18630.018 Da / Num. of mol.: 2 / Fragment: DPP1 HEAVY CHAIN, RESIDUES 230-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN / DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 7583.444 Da / Num. of mol.: 2 / Fragment: DPP1 LIGHT CHAIN, RESIDUES 371-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 2 types, 4 molecules

#4: 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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 98 molecules

#6: Chemical ChemComp-GDI / (2S)-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]PIPERIDINE-2-CARBOXAMIDE


Mass: 360.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N4O
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.81 % / Description: NONE
Crystal growDetails: 21% PEG3350, 200MM AMSO4, 100MM NA ACCETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1.0723
DetectorDetector: CCD / Date: May 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.35→44.1 Å / Num. obs: 38846 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3B

1k3b


Resolution: 2.35→44.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 14.103 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22302 1863 5 %RANDOM
Rwork0.18735 ---
obs0.18915 35300 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.13 Å20 Å2
2--0.13 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 126 94 5700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195787
X-RAY DIFFRACTIONr_bond_other_d0.0010.025110
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9487861
X-RAY DIFFRACTIONr_angle_other_deg0.7143.00411712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00423.941269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04115857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9631520
X-RAY DIFFRACTIONr_chiral_restr0.0670.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021418
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_it1.6493.9192761
X-RAY DIFFRACTIONr_mcbond_other1.6493.9182760
X-RAY DIFFRACTIONr_mcangle_it2.6146.5993439
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2384.3013026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 132 -
Rwork0.271 2379 -
obs--89.01 %
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)
12.0004-0.04150.0832.48710.22590.8156-0.2729-0.18930.5504-0.17130.1114-0.2582-0.41920.18330.16150.2914-0.1597-0.11320.2283-0.06010.26832.917-1.838938.8938
22.5924-0.00680.31661.69740.21171.459-0.11340.0844-0.3535-0.02280.1186-0.33710.06090.3525-0.00510.0637-0.03460.01610.2266-0.05250.217940.3127-25.762336.1522
32.36480.5033-0.05710.9972-0.22541.2412-0.0952-0.2573-0.5330.20290.0245-0.37550.16430.27940.07070.15110.0611-0.01290.27070.0230.302338.7733-29.53745.9457
43.81260.85430.97514.32390.12822.736-0.23610.8901-0.3147-0.77910.3035-0.2380.11820.4176-0.06740.3744-0.16730.03870.3967-0.0730.033319.4621-26.02510.3084
52.72830.62470.67392.91150.29581.3981-0.31190.41890.7727-0.55810.11660.4272-0.35690.03980.19530.4169-0.147-0.23670.17070.15680.29068.6585-3.57815.5758
62.8540.67890.60793.03550.14061.4028-0.37290.12220.7301-0.63850.13320.9946-0.3901-0.21440.23970.3788-0.0655-0.33560.14820.10340.4643-1.5317-6.390316.9864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B206 - 370
3X-RAY DIFFRACTION3C371 - 439
4X-RAY DIFFRACTION4D1 - 119
5X-RAY DIFFRACTION5E206 - 369
6X-RAY DIFFRACTION6F371 - 439

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