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- PDB-5mrv: Crystal structure of human carboxypeptidase O in complex with NvCI -

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Basic information

Entry
Database: PDB / ID: 5mrv
TitleCrystal structure of human carboxypeptidase O in complex with NvCI
Components
  • Carboxypeptidase O
  • Metallocarboxypeptidase inhibitor
KeywordsHYDROLASE / Digestive Metallocarboxypeptidase / food digestion / carboxypeptidase inhibitor / Brush Border enzyme
Function / homology
Function and homology information


: / metalloendopeptidase inhibitor activity / negative regulation of endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / apical plasma membrane / proteolysis / extracellular space / zinc ion binding / metal ion binding
Similarity search - Function
Laminin - #90 / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Laminin / Aminopeptidase / Ribbon / 3-Layer(aba) Sandwich ...Laminin - #90 / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Laminin / Aminopeptidase / Ribbon / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Metallocarboxypeptidase inhibitor / Carboxypeptidase O
Similarity search - Component
Biological speciesHomo sapiens (human)
Nerita versicolor (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsGarcia-Pardo, J. / Garcia-Guerrero, M.C. / Fernandez-Alvarez, R. / Lyons, P. / Aviles, F.X. / Lorenzo, J. / Reverter, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structure and mechanism of human carboxypeptidase O: Insights into its specific activity for acidic residues.
Authors: Garcia-Guerrero, M.C. / Garcia-Pardo, J. / Berenguer, E. / Fernandez-Alvarez, R. / Barfi, G.B. / Lyons, P.J. / Aviles, F.X. / Huber, R. / Lorenzo, J. / Reverter, D.
History
DepositionDec 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase O
B: Carboxypeptidase O
C: Metallocarboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,00910
Polymers87,7723
Non-polymers1,2377
Water9,386521
1
A: Carboxypeptidase O
C: Metallocarboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5946
Polymers46,8652
Non-polymers7294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-36 kcal/mol
Surface area14840 Å2
MethodPISA
2
B: Carboxypeptidase O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4164
Polymers40,9081
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-32 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.114, 72.144, 90.187
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carboxypeptidase O / CPO


Mass: 40907.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPO / Plasmid: pTriEx-7 vector / Cell line (production host): HEK293 F / Production host: Homo sapiens (human)
References: UniProt: Q8IVL8, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Metallocarboxypeptidase inhibitor / MCPI / Carboxypeptidase inhibitor / NvCI


Mass: 5956.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Carboxypeptidase Inhibitor obtained from the marine snail Nerita versicolor
Source: (gene. exp.) Nerita versicolor (invertebrata) / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P86912
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Homo sapiens (human) / Gene: CPO / Plasmid: pTriEx-7 vector / Cell line (production host): HEK293 F / Production host: Homo sapiens (human)
#4: 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.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Gene: CPO / Plasmid: pTriEx-7 vector / Cell line (production host): HEK293 F / Production host: Homo sapiens (human)
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.74 Å3/Da / Density % sol: 55.08 % / Description: Monoclinic crystals C 1 2 1
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Drops were prepared by mixing equal volumes of protein solution (CPO:NvCI molar ratio, 1:0.5) at 5 mg/ml (in 5 mM Tris-HCl pH 7.3, 100 mM NaCl, 1 mM B-mercaptoetanol) and reservoir solution ...Details: Drops were prepared by mixing equal volumes of protein solution (CPO:NvCI molar ratio, 1:0.5) at 5 mg/ml (in 5 mM Tris-HCl pH 7.3, 100 mM NaCl, 1 mM B-mercaptoetanol) and reservoir solution containning HEPES pH 7.0, 200 mM ammonium choride and 20% PEG6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.854→64.984 Å / Num. obs: 79948 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rsym value: 0.084 / Net I/σ(I): 13.9
Reflection shellResolution: 1.854→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / CC1/2: 0.68 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PCU

2pcu


Resolution: 1.854→59.947 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.19
RfactorNum. reflection% reflection
Rfree0.2082 3961 4.96 %
Rwork0.1846 --
obs0.1857 79833 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.854→59.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 0 521 5995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115660
X-RAY DIFFRACTIONf_angle_d0.967706
X-RAY DIFFRACTIONf_dihedral_angle_d13.6923326
X-RAY DIFFRACTIONf_chiral_restr0.056816
X-RAY DIFFRACTIONf_plane_restr0.006983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.854-1.87660.39751380.36572657X-RAY DIFFRACTION97
1.8766-1.90040.33411350.3192652X-RAY DIFFRACTION97
1.9004-1.92540.34511430.2922662X-RAY DIFFRACTION97
1.9254-1.95180.32761500.26742686X-RAY DIFFRACTION97
1.9518-1.97970.29741240.25372704X-RAY DIFFRACTION98
1.9797-2.00920.25951290.23722658X-RAY DIFFRACTION97
2.0092-2.04060.25571350.22312715X-RAY DIFFRACTION98
2.0406-2.07410.23051410.22932701X-RAY DIFFRACTION98
2.0741-2.10980.25961420.21972692X-RAY DIFFRACTION98
2.1098-2.14820.24381470.21142723X-RAY DIFFRACTION99
2.1482-2.18950.23531630.20662689X-RAY DIFFRACTION97
2.1895-2.23420.24711680.19242652X-RAY DIFFRACTION99
2.2342-2.28280.22181200.19962666X-RAY DIFFRACTION98
2.2828-2.33590.24581410.19262725X-RAY DIFFRACTION98
2.3359-2.39430.22051490.18652772X-RAY DIFFRACTION99
2.3943-2.4590.20761480.19262707X-RAY DIFFRACTION99
2.459-2.53140.2281480.18612711X-RAY DIFFRACTION98
2.5314-2.61310.26021440.18632714X-RAY DIFFRACTION99
2.6131-2.70650.20181520.19442715X-RAY DIFFRACTION98
2.7065-2.81490.21081370.19222747X-RAY DIFFRACTION99
2.8149-2.9430.18321300.17982740X-RAY DIFFRACTION99
2.943-3.09810.20291210.17812740X-RAY DIFFRACTION98
3.0981-3.29220.20681520.17542697X-RAY DIFFRACTION97
3.2922-3.54640.17691460.16772707X-RAY DIFFRACTION98
3.5464-3.90320.16131420.14672687X-RAY DIFFRACTION97
3.9032-4.46790.13841330.14422731X-RAY DIFFRACTION98
4.4679-5.62840.16991480.14762778X-RAY DIFFRACTION99
5.6284-59.97790.2021350.17622844X-RAY DIFFRACTION98

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