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- PDB-1qmu: Duck carboxypeptidase D domain II -

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Basic information

Entry
Database: PDB / ID: 1qmu
TitleDuck carboxypeptidase D domain II
ComponentsCARBOXYPEPTIDASE GP180 RESIDUES 503-882
KeywordsCARBOXYPEPTIDASE / HYDROLASE / ZINC-DEPENDENT PROTEASE
Function / homology
Function and homology information


metallocarboxypeptidase D / peptide metabolic process / metallocarboxypeptidase activity / protein processing / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carboxypeptidase D, carboxypeptidase-like domain 3 / Carboxypeptidase D, carboxypeptidase-like domain 2 / 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. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A ...Carboxypeptidase D, carboxypeptidase-like domain 3 / Carboxypeptidase D, carboxypeptidase-like domain 2 / 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. / Peptidase family M14 domain profile. / 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 D / Carboxypeptidase D
Similarity search - Component
Biological speciesLOPHONETTA SPECULARIOIDES (crested duck)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsGomis-Rueth, F.X. / Coll, M. / Aviles, F.X. / Vendrell, J. / Fricker, L.D.
CitationJournal: Embo J. / Year: 1999
Title: Crystal Structure of Avian Carboxypeptidase D Domain II : A Prototype for the Regulatory Metallocarboxypeptidase Subfamily
Authors: Gomis-Rueth, F.X. / Companys, V. / Qian, Y. / Fricker, L.D. / Vendrell, J. / Aviles, F.X. / Coll, M.
History
DepositionOct 6, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _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
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: CARBOXYPEPTIDASE GP180 RESIDUES 503-882
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2888
Polymers43,3371
Non-polymers1,9517
Water2,180121
1
A: CARBOXYPEPTIDASE GP180 RESIDUES 503-882
hetero molecules

A: CARBOXYPEPTIDASE GP180 RESIDUES 503-882
hetero molecules

A: CARBOXYPEPTIDASE GP180 RESIDUES 503-882
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,86524
Polymers130,0123
Non-polymers5,85321
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area3230 Å2
ΔGint-0.3 kcal/mol
Surface area55770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)135.540, 135.540, 135.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CARBOXYPEPTIDASE GP180 RESIDUES 503-882


Mass: 43337.297 Da / Num. of mol.: 1 / Fragment: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LOPHONETTA SPECULARIOIDES (crested duck)
Description: OBTAINED AFTER CLONING INTO AND OVEREXPRESSION FROM A PICHIA PASTORIS SYSTEM.
Organ: LIVER / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71 / References: UniProt: Q90240, UniProt: P83852*PLUS

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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

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Non-polymers , 3 types, 125 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 73 %
Crystal growpH: 5.2 / Details: pH 5.20
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mMTris-HCl1drop
350 mM1dropNaCl
40.5 mMbenzamidine1drop
52.1 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8467
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8467 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 22564 / % possible obs: 98 % / Redundancy: 12 % / Biso Wilson estimate: 83.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.2 / % possible all: 87
Reflection
*PLUS
Num. measured all: 270100
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→20 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 -7 %RANDOM
Rwork0.198 ---
obs0.198 22539 98.1 %-
Solvent computationBsol: 31.47 Å2 / ksol: 0.298 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 122 121 3300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.198 / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS

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