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- PDB-2nsm: Crystal structure of the human carboxypeptidase N (Kininase I) ca... -

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Basic information

Entry
Database: PDB / ID: 2nsm
TitleCrystal structure of the human carboxypeptidase N (Kininase I) catalytic domain
ComponentsCarboxypeptidase N catalytic chain
KeywordsHYDROLASE / caroxypeptidase / zinc peptidase / transthyretin-like domain / hormone processing / peptide modification
Function / homology
Function and homology information


lysine carboxypeptidase / peptide metabolic process / regulation of complement activation / bradykinin catabolic process / metallocarboxypeptidase activity / response to glucocorticoid / Regulation of Complement cascade / protein processing / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Carboxypeptidase N, N-terminal domain / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases ...Carboxypeptidase N, N-terminal domain / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carboxypeptidase N catalytic chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKeil, C. / Maskos, K. / Than, M. / Hoopes, J.T. / Huber, R. / Tan, F. / Deddish, P.A. / Erdoes, E.G. / Skidgel, R.A. / Bode, W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain
Authors: Keil, C. / Maskos, K. / Than, M. / Hoopes, J.T. / Huber, R. / Tan, F. / Deddish, P.A. / Erdoes, E.G. / Skidgel, R.A. / Bode, W.
History
DepositionNov 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxypeptidase N catalytic chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2328
Polymers50,1841
Non-polymers1,0487
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.030, 150.030, 54.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Carboxypeptidase N catalytic chain / CPN / Carboxypeptidase N polypeptide 1 / Carboxypeptidase N small subunit / Lysine carboxypeptidase ...CPN / Carboxypeptidase N polypeptide 1 / Carboxypeptidase N small subunit / Lysine carboxypeptidase / Arginine carboxypeptidase / Kininase-1 / Serum carboxypeptidase N / SCPN / Anaphylatoxin inactivator / Plasma carboxypeptidase B


Mass: 50184.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P15169, lysine carboxypeptidase
#2: 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 / N-Acetylglucosamine


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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 2M Ammonium sulfate, 5mM EDTA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Details: mirrors
RadiationMonochromator: Si(111) double crystal, non dispersive / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 41723 / Num. obs: 41723 / % possible obs: 99.4 % / Observed criterion σ(F): 4.37 / Observed criterion σ(I): 4.37 / Redundancy: 3.36 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15.26
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.37 / Num. unique all: 41723 / Rsym value: 0.28 / % possible all: 99.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1H8L

1h8l


Resolution: 2.1→20 Å / σ(F): 4.37 / σ(I): 4.37 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2008 2069 -
Rwork0.1789 --
obs0.1789 40803 98.3 %
all-41528 -
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 62 370 3569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.1→2.17 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.2008 2069 -
Rwork0.1789 --
obs--98.3 %

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