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- PDB-4q7z: Neutrophil serine protease 4 (PRSS57) with phe-phe-arg-chlorometh... -

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Basic information

Entry
Database: PDB / ID: 4q7z
TitleNeutrophil serine protease 4 (PRSS57) with phe-phe-arg-chloromethylketone (FFR-cmk)
ComponentsSerine protease 57
KeywordsHYDROLASE/HYDROLASE INHIBITOR / trypsin homology / peptidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / azurophil granule lumen / heparin binding / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHE-PHE-ARG-chloromethylketone / Chem-2YT / Serine protease 57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEigenbrot, C. / Lin, S.J. / Dong, K.C.
CitationJournal: Structure / Year: 2014
Title: Structures of neutrophil serine protease 4 reveal an unusual mechanism of substrate recognition by a trypsin-fold protease.
Authors: Lin, S.J. / Dong, K.C. / Eigenbrot, C. / van Lookeren Campagne, M. / Kirchhofer, D.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 22, 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_molecule / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_molecule.asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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: Serine protease 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2226
Polymers27,0031
Non-polymers1,2195
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.986, 64.466, 68.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine protease 57 / Serine protease 1-like protein 1


Mass: 27002.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS57, PRSSL1, UNQ782/PRO1599 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6UWY2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 249 molecules

#4: Chemical ChemComp-2YT / L-phenylalanyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide / PHE-PHE-ARG-chloromethylketone


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 503.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35ClN6O3 / References: PHE-PHE-ARG-chloromethylketone
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNATURAL VARIANT DESCRIBED IN THE UNIPROT ENTRY Q6UWY2

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG-MME 2000, 0.1 M Tris 8.5, 0.2 M trimethylamine N-oxide, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127092 Å / Relative weight: 1
ReflectionResolution: 1.4→46.92 Å / Num. all: 45664 / Num. obs: 45530 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.048 / Net I/σ(I): 34.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE

1hne


Resolution: 1.4→46.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.081 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21472 2276 5 %RANDOM
Rwork0.19244 ---
all0.21 45530 --
obs0.19352 43254 93.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0 Å2
2---0.08 Å20 Å2
3----0.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.069 Å
Refinement stepCycle: LAST / Resolution: 1.4→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 79 246 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191954
X-RAY DIFFRACTIONr_bond_other_d0.0010.021330
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9752664
X-RAY DIFFRACTIONr_angle_other_deg0.8683.0053170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.05620.3781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69615280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1361523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212169
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
LS refinement shellResolution: 1.4→1.476 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 334 -
Rwork0.323 6072 -
obs--97.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23210.0290.01670.22020.02540.4741-0.00960.01450.0164-0.0103-0.0325-0.0511-0.0329-0.00230.04210.0276-0.00010.00590.0161-0.00250.0345-9.72686.88948.4884
20.2458-0.10620.13550.2892-0.03180.40990.00650.0113-0.00730.0234-0.0539-0.06420.03420.03760.04740.0224-0.00530.00720.02010.01110.0433-5.093-1.388712.1689
31.02750.34940.07530.2780.5081.46940.0593-0.0786-0.09610.097-0.1128-0.01670.2515-0.29340.05350.0687-0.05980.01940.0647-0.00760.0206-20.8268-7.072920.9746
40.13790.106-0.00460.1291-0.01270.6309-0.037-0.01570.0072-0.0134-0.0154-0.03320.0885-0.16440.05240.0324-0.0225-0.00140.046-0.01510.0369-20.72-4.77579.0689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 67
2X-RAY DIFFRACTION2A68 - 110
3X-RAY DIFFRACTION3A111 - 128
4X-RAY DIFFRACTION4A129 - 233

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