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- PDB-1z5r: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B -

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Basic information

Entry
Database: PDB / ID: 1z5r
TitleCrystal Structure of Activated Porcine Pancreatic Carboxypeptidase B
Componentsprocarboxypeptidase B
KeywordsHYDROLASE / carboxypeptidase B / exopeptidase
Function / homology
Function and homology information


carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase B, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / 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 ...Carboxypeptidase B, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAdler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase b.
Authors: Adler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M.
History
DepositionMar 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: procarboxypeptidase B
B: procarboxypeptidase B
C: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4166
Polymers104,2203
Non-polymers1963
Water18,8441046
1
A: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8052
Polymers34,7401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8052
Polymers34,7401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8052
Polymers34,7401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.815, 96.055, 135.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein procarboxypeptidase B


Mass: 34739.859 Da / Num. of mol.: 3 / Fragment: Catalytic Domain / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09955, carboxypeptidase B
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium chloride, Tris, MGTA, sodium cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2002 / Details: Flat Mirror
RadiationMonochromator: single crystal SI(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 171969 / Num. obs: 161497 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.038 / Net I/σ(I): 19.4
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 28332 / Rsym value: 0.262 / % possible all: 72.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
X-GENdata reduction
MOLREPphasing
X-PLOR3.1refinement
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAS catalytic domain

1nas


Resolution: 1.4→8 Å / Isotropic thermal model: Overall / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 6484 -RANDOM
Rwork0.175 ---
all0.189 170912 --
obs0.177 160654 94 %-
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.191 Å20 Å20 Å2
2---0.673 Å20 Å2
3---0.482 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 3 1046 8357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.86
X-RAY DIFFRACTIONx_improper_angle_d1.32
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4-1.460.2634340.27104121084668.1
1.46-1.540.2416730.2351652893.2
1.54-1.640.2247570.2151845897.3
1.64-1.760.2217550.2051930597.8
1.76-1.940.2158830.1942004798.2
1.94-2.210.2018580.1842072198.7
2.21-2.770.2058720.1652118099.2
2.77-80.28020.1462170999

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