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- PDB-4q7x: Neutrophil serine protease 4 (PRSS57) apo form 1 -

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Basic information

Entry
Database: PDB / ID: 4q7x
TitleNeutrophil serine protease 4 (PRSS57) apo form 1
ComponentsSerine protease 57
KeywordsHYDROLASE / trypsin homology / peptidase
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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_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_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_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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease 57
B: Serine protease 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4599
Polymers54,0062
Non-polymers1,4537
Water1,964109
1
A: Serine protease 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7765
Polymers27,0031
Non-polymers7734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine protease 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6844
Polymers27,0031
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.366, 70.366, 150.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 27002.900 Da / Num. of mol.: 2
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
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
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.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 16% PEG 10,000, 0.1M sodium/ammonium acetate, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 23577 / Num. obs: 23565 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 63.62 Å2 / Rsym value: 0.082 / Net I/σ(I): 14.1

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Processing

Software
NameVersionClassification
BOSdata collection
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE

1hne


Resolution: 2.55→49.76 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1203 5.11 %RANDOM
Rwork0.1971 ---
all0.2 23577 --
obs0.1988 23565 99.27 %-
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.717 Å20 Å20 Å2
2---8.717 Å20 Å2
3---17.4341 Å2
Refine analyzeLuzzati coordinate error obs: 0.379 Å
Refinement stepCycle: LAST / Resolution: 2.55→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 94 109 3775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093780HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055157HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1257SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes581HARMONIC5
X-RAY DIFFRACTIONt_it3780HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion16.07
X-RAY DIFFRACTIONt_chiral_improper_torsion484SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4204SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.66 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3042 142 4.99 %
Rwork0.2345 2702 -
all0.2378 2844 -
obs--99.27 %
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)
12.9602-0.36240.63442.358-1.25844.0901-0.06-0.1293-0.26190.54420.08010.1935-0.0287-0.1988-0.02010.1608-0.07580.0935-0.20920.0029-0.106113.8773-28.529911.4683
22.19960.3032-0.20143.1276-2.10581.5151-0.0996-0.1043-0.15450.36290.18490.3345-0.1072-0.1932-0.08520.0313-0.02960.1057-0.20040.0114-0.02888.664-24.80433.6402
30-0.1991-1.11563.15480.17590.8988-0.00230.14810.08690.05470.0052-0.1221-0.05560.0417-0.00290.0985-0.1296-0.0359-0.10590.09-0.074524.0757-17.6115-3.7652
41.3456-0.94480.75413.7094-1.22222.9155-0.07280.2291-0.05450.425-0.1678-0.15010.06330.390.2406-0.0153-0.095-0.0224-0.12610.0266-0.086122.7131-28.1984-1.2363
53.4849-0.04140.81462.59531.62674.5285-0.02330.1784-0.1908-0.54420.0668-0.1675-0.12150.2092-0.04350.15460.03680.087-0.22420.0061-0.111421.31356.6491-2.8077
61.666-0.09610.2342.86181.77421.1538-0.09030.1239-0.1235-0.32220.1839-0.3069-0.12350.1904-0.09360.02570.04040.1098-0.1663-0.0178-0.022426.525210.384.9839
701.21210.05151.5037-0.52631.30270.0008-0.09920.1014-0.0185-0.01570.0905-0.047-0.00590.01480.0690.1493-0.0698-0.0863-0.1252-0.050211.089917.725212.3301
81.17850.96090.87653.53761.20892.9453-0.0714-0.1929-0.0274-0.3857-0.18820.22660.1024-0.47010.2596-0.00660.0908-0.0182-0.1138-0.0419-0.066311.71186.659910.0113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|16 - A|67 }A16 - 67
2X-RAY DIFFRACTION2{ A|68 - A|110 }A68 - 110
3X-RAY DIFFRACTION3{ A|111 - A|128 }A111 - 128
4X-RAY DIFFRACTION4{ A|129 - A|235 }A129 - 235
5X-RAY DIFFRACTION5{ B|16 - B|67 }B16 - 67
6X-RAY DIFFRACTION6{ B|68 - B|110 }B68 - 110
7X-RAY DIFFRACTION7{ B|111 - B|128 }B111 - 128
8X-RAY DIFFRACTION8{ B|129 - B|232 }B129 - 232

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