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- PDB-3n2z: The Structure of Human Prolylcarboxypeptidase at 2.80 Angstroms R... -

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Basic information

Entry
Database: PDB / ID: 3n2z
TitleThe Structure of Human Prolylcarboxypeptidase at 2.80 Angstroms Resolution
ComponentsLysosomal Pro-X carboxypeptidase
KeywordsHYDROLASE / alpha/beta hydrolase / PrCP / serine carboxypeptidase
Function / homology
Function and homology information


lysosomal Pro-Xaa carboxypeptidase / plasma kallikrein-kinin cascade / serine-type carboxypeptidase activity / neutrophil degranulation / blood coagulation, intrinsic pathway / regulation of blood vessel endothelial cell migration / basal part of cell / angiogenesis involved in wound healing / negative regulation of systemic arterial blood pressure / dipeptidyl-peptidase activity ...lysosomal Pro-Xaa carboxypeptidase / plasma kallikrein-kinin cascade / serine-type carboxypeptidase activity / neutrophil degranulation / blood coagulation, intrinsic pathway / regulation of blood vessel endothelial cell migration / basal part of cell / angiogenesis involved in wound healing / negative regulation of systemic arterial blood pressure / dipeptidyl-peptidase activity / regulation of thyroid hormone receptor signaling pathway / regulation of reactive oxygen species metabolic process / azurophil granule membrane / ficolin-1-rich granule membrane / energy homeostasis / Intrinsic Pathway of Fibrin Clot Formation / glucose homeostasis / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular exosome / plasma membrane
Similarity search - Function
Serine carboxypeptidase S28, SKS domain / Serine carboxypeptidase S28, SKS domain / Peptidase S28 / Serine carboxypeptidase S28 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Serine carboxypeptidase S28, SKS domain / Serine carboxypeptidase S28, SKS domain / Peptidase S28 / Serine carboxypeptidase S28 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Lysosomal Pro-X carboxypeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.79 Å
AuthorsSoisson, S.M. / Patel, S.B. / Lumb, K.J. / Sharma, S.
CitationJournal: Bmc Struct.Biol. / Year: 2010
Title: Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase.
Authors: Soisson, S.M. / Patel, S.B. / Abeywickrema, P.D. / Bryne, N.J. / Diehl, R.E. / Hall, D.L. / Ford, R.E. / Reid, J.C. / Rickert, K.W. / Shipman, J.M. / Sharma, S. / Lumb, K.J.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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
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
B: Lysosomal Pro-X carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9767
Polymers50,5711
Non-polymers1,4056
Water1,36976
1
B: Lysosomal Pro-X carboxypeptidase
hetero molecules

B: Lysosomal Pro-X carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,95314
Polymers101,1422
Non-polymers2,81112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area6950 Å2
ΔGint-3 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.140, 181.140, 240.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Lysosomal Pro-X carboxypeptidase / Prolylcarboxypeptidase / PRCP / Proline carboxypeptidase / Angiotensinase C / Lysosomal carboxypeptidase C


Mass: 50571.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRCP, PCP / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P42785, lysosomal Pro-Xaa carboxypeptidase
#2: 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
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M Ammonium Sulfate, 0.1M HEPES, 1-2% PEG400 mixed in a 2:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 10.2 % / Av σ(I) over netI: 26.78 / Number: 671445 / Rmerge(I) obs: 0.138 / Χ2: 1.78 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 66048 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.155010010.061.94110.1
5.677.1510010.0882.0839.4
4.965.6710010.1012.2279.5
4.54.9610010.0992.2939.2
4.184.510010.1192.3319.7
3.944.1810010.1472.49810.1
3.743.9410010.1772.29610.5
3.583.7410010.2112.0210.8
3.443.5899.910.2351.77210.9
3.323.4410010.2981.6211
3.223.3210010.3691.34511
3.123.2210010.4831.17310.9
3.043.1210010.5161.10810.8
2.973.0410010.6571.1110.7
2.92.9798.210.7661.0418
ReflectionResolution: 2.79→50 Å / Num. obs: 37814 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Rmerge(I) obs: 0.098 / Χ2: 1.189 / Net I/σ(I): 9.9
Reflection shellResolution: 2.79→2.87 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.594 / Num. unique all: 2513 / Χ2: 1.098 / % possible all: 100

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
BUSTER2.9.4refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.79→47.67 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1875 4.99 %RANDOM
Rwork0.216 ---
obs0.218 37540 99.19 %-
all-37897 --
Displacement parametersBiso max: 141.06 Å2 / Biso mean: 64.574 Å2 / Biso min: 32.56 Å2
Baniso -1Baniso -2Baniso -3
1--16.027 Å20 Å20 Å2
2---16.027 Å20 Å2
3---32.055 Å2
Refine analyzeLuzzati coordinate error obs: 0.433 Å
Refinement stepCycle: LAST / Resolution: 2.79→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 89 76 3704
LS refinement shellResolution: 2.79→2.87 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.352 136 4.79 %
Rwork0.315 2703 -
all0.317 2839 -
obs--99.19 %

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