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- PDB-4oem: Crystal structure of Cathepsin C in complex with dipeptide substrates -

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Basic information

Entry
Database: PDB / ID: 4oem
TitleCrystal structure of Cathepsin C in complex with dipeptide substrates
Components(Dipeptidyl peptidase 1 ...) x 2
KeywordsHYDROLASE / beta barrel / dipeptidyl aminopeptidase I
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 / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...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 / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / 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 / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLYCINE / LYSINE / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsZhao, B. / Smallwood, A. / Concha, N.
CitationJournal: Biochemistry / Year: 2012
Title: The amino-acid substituents of dipeptide substrates of cathepsin C can determine the rate-limiting steps of catalysis.
Authors: Rubach, J.K. / Cui, G. / Schneck, J.L. / Taylor, A.N. / Zhao, B. / Smallwood, A. / Nevins, N. / Wisnoski, D. / Thrall, S.H. / Meek, T.D.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 1 Heavy chain
B: Dipeptidyl peptidase 1 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,01613
Polymers49,7502
Non-polymers1,26611
Water5,837324
1
A: Dipeptidyl peptidase 1 Heavy chain
B: Dipeptidyl peptidase 1 Light chain
hetero molecules

A: Dipeptidyl peptidase 1 Heavy chain
B: Dipeptidyl peptidase 1 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,03126
Polymers99,5004
Non-polymers2,53122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area19280 Å2
ΔGint-117 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.920, 89.016, 115.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Dipeptidyl peptidase 1 ... , 2 types, 2 molecules AB

#1: Protein Dipeptidyl peptidase 1 Heavy chain / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPP-I / DPPI / Dipeptidyl transferase


Mass: 42037.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPPI, CTSC / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein Dipeptidyl peptidase 1 Light chain / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPP-I / DPPI / Dipeptidyl transferase


Mass: 7712.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 1 types, 3 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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 , 6 types, 332 molecules

#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 16-26% polyethylene glycol-3350 at pH 6.0-6.9 in 200 mM MgCl2, 100 mM Bis-Tris buffer, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP
PH range: 6.0 - 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 86821 / Num. obs: 85432 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.063 / Net I/σ(I): 12.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.22 / Rsym value: 0.59 / % possible all: 88.7

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.52→27.49 Å / Cor.coef. Fo:Fc: 0.9642 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 3759 5.92 %RANDOM
Rwork0.1641 ---
obs0.1649 63506 94.47 %-
all-86821 --
Displacement parametersBiso mean: 26.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.2294 Å20 Å20 Å2
2---0.677 Å20 Å2
3----0.5525 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.52→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 77 324 3128
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015439HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.049685HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1146SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes842HARMONIC5
X-RAY DIFFRACTIONt_it5439HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.55
X-RAY DIFFRACTIONt_other_torsion15.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3635SEMIHARMONIC4
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2835 220 5.68 %
Rwork0.2341 3656 -
all0.2367 3876 -
obs--94.47 %
Refinement TLS params.Method: refined / Origin x: 32.5449 Å / Origin y: 16.2029 Å / Origin z: 16.6665 Å
111213212223313233
T-0.0281 Å2-0.0021 Å20.0324 Å2--0.0637 Å2-0.0205 Å2---0.0655 Å2
L0.8658 °2-0.1121 °20.0588 °2-0.7848 °20.07 °2--0.7043 °2
S0.008 Å °0.0033 Å °0.0037 Å °0.0935 Å °-0.018 Å °0.0729 Å °-0.1193 Å °-0.0704 Å °0.01 Å °
Refinement TLS groupSelection details: { A|* }

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