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- PDB-1yxa: Serpina3n, a murine orthologue of human antichymotrypsin -

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Basic information

Entry
Database: PDB / ID: 1yxa
TitleSerpina3n, a murine orthologue of human antichymotrypsin
Componentsserine (or cysteine) proteinase inhibitor, clade A, member 3N
KeywordsHYDROLASE INHIBITOR / Serpin / antichymotrypsin / protease inhibitor / reactive centre loop / plasma
Function / homology
Function and homology information


response to cytokine / acute-phase response / response to bacterium / serine-type endopeptidase inhibitor activity / response to peptide hormone / extracellular space / extracellular region
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease inhibitor A3N
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHorvath, A.J. / Irving, J.A. / Law, R.H. / Rossjohn, J. / Bottomley, S.P. / Quinsey, N.S. / Pike, R.N. / Coughlin, P.B. / Whisstock, J.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The murine orthologue of human antichymotrypsin: a structural paradigm for clade A3 serpins.
Authors: Horvath, A.J. / Irving, J.A. / Rossjohn, J. / Law, R.H. / Bottomley, S.P. / Quinsey, N.S. / Pike, R.N. / Coughlin, P.B. / Whisstock, J.C.
History
DepositionFeb 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct_biol
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: serine (or cysteine) proteinase inhibitor, clade A, member 3N
B: serine (or cysteine) proteinase inhibitor, clade A, member 3N


Theoretical massNumber of molelcules
Total (without water)89,5872
Polymers89,5872
Non-polymers00
Water7,134396
1
A: serine (or cysteine) proteinase inhibitor, clade A, member 3N


Theoretical massNumber of molelcules
Total (without water)44,7931
Polymers44,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: serine (or cysteine) proteinase inhibitor, clade A, member 3N


Theoretical massNumber of molelcules
Total (without water)44,7931
Polymers44,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.340, 92.620, 118.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA52 - 10632 - 86
21THRTHRTHRTHRBB52 - 10632 - 86
32ILEILELYSLYSAA133 - 156113 - 136
42ILEILELYSLYSBB133 - 156113 - 136
53LEULEUGLUGLUAA158 - 192138 - 172
63LEULEUGLUGLUBB158 - 192138 - 172
74ASPASPCYSCYSAA198 - 231178 - 211
84ASPASPCYSCYSBB198 - 231178 - 211
95PROPROALAALAAA236 - 371216 - 351
105PROPROALAALABB236 - 371216 - 351
116LEULEULYSLYSAA388 - 418368 - 398
126LEULEULYSLYSBB388 - 418368 - 398
DetailsEach chain represents a separate biological unit.

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Components

#1: Protein serine (or cysteine) proteinase inhibitor, clade A, member 3N / antichymotrypsin / Serpina3n


Mass: 44793.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-3a(His) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q91WP6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M Na tartarate, 0.1M HEPES, 24% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2004 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 62513 / Num. obs: 57467 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Χ2: 1.779 / Net I/σ(I): 15.59
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.10.41544802.306172.9
2.07-2.152.40.38351602.139184.1
2.15-2.252.70.34355762.216191
2.25-2.372.90.30358442.092194.8
2.37-2.523.20.25159952.041197.3
2.52-2.713.50.19761112.002198.9
2.71-2.993.60.13661271.912198.7
2.99-3.423.70.07661131.684198.2
3.42-4.313.60.04361031.308196.7
4.31-1003.60.03459580.976191

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.621 / Cor.coef. Fo:Fc: 0.21
Highest resolutionLowest resolution
Rotation3.5 Å30.02 Å
Translation3.5 Å30.02 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOLREP8.2.01version5.0:04/07/04phasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1.401data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLP DIFFERENCES TO ALA

1qlp


Resolution: 2.1→30.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.755 / SU ML: 0.152 / SU R Cruickshank DPI: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.205 / ESU R Free: 0.179 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2086 4.1 %RANDOM
Rwork0.193 ---
all0.195 54092 --
obs0.195 51453 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2--3.82 Å20 Å2
3----2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.179 Å0.205 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5723 0 0 396 6119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225852
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9797947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27325.084238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.725151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3021521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024330
X-RAY DIFFRACTIONr_nbd_refined0.1990.22553
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2390
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.222
X-RAY DIFFRACTIONr_mcbond_it1.58833810
X-RAY DIFFRACTIONr_mcangle_it2.65655998
X-RAY DIFFRACTIONr_scbond_it4.15472280
X-RAY DIFFRACTIONr_scangle_it5.99591949
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1264MEDIUM POSITIONAL0.1890.5
1205LOOSE POSITIONAL0.4635
1264MEDIUM THERMAL1.113
1205LOOSE THERMAL2.3510
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 131 -
Rwork0.295 3241 -
obs-3351 85.4 %
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)
12.46131.4073-3.380917.9113.89356.6286-0.1621-0.22940.1324-0.0098-0.0685-0.17930.14761.05510.2305-0.07090.001-0.03620.04290.039-0.0467.46439.860545.6499
224.552.572-22.10820.6006-0.134334.28520.94360.41521.7826-0.65080.8801-0.66071.1954-1.7039-1.82370.0838-0.06930.1551-0.39690.37780.501255.771627.670736.8581
39.602214.2672-12.221621.5245-17.500716.8858-0.43120.69920.224-0.28191.08530.9369-0.4266-2.4567-0.6541-0.06190.17110.04060.25590.14180.066243.739348.761131.8413
43.29745.24811.333415.06973.42472.4798-0.04390.1195-0.0613-0.12110.2525-0.27930.19430.5653-0.2086-0.04190.0494-0.00860.0555-0.0002-0.113423.450436.157342.8251
57.96471.2789-8.41853.83552.024614.21890.3426-0.3669-0.13690.1766-0.23970.11270.4937-0.1963-0.10290.0147-0.0373-0.052-0.0765-0.0147-0.034510.921827.803933.0758
617.317515.2779-10.301717.7783-14.94814.1137-0.4235-0.2030.1361-0.57140.50610.214-0.372-0.9797-0.0826-0.10010.12060.027-0.01860.0518-0.12984.02152.229928.7577
70.54890.4127-0.86080.3115-0.70464.26080.06090.08710.0989-0.04250.12550.0224-0.2421-0.596-0.1864-0.01170.0190.0173-0.01980.03360.028250.987243.35941.1024
80.48730.2163-0.62290.1241-0.60834.70770.04510.0407-0.0362-0.0102-0.0084-0.0121-0.2524-0.1864-0.0368-0.02360.0180.01620.00390.0260.00829.407645.05438.1031
91.7997-0.52310.16230.15660.05342.246-0.0211-0.09280.0791-0.01020.1151-0.07140.1414-0.0129-0.0940.0282-0.0026-0.0089-0.0884-0.0049-0.006959.618137.177457.4588
100.7002-0.64680.23450.7408-0.07082.25330.05280.08530.00680.01710.0410.02110.20880.094-0.09380.0219-0.0219-0.0021-0.05450.0133-0.0115.691537.508254.8937
110.86850.63070.06392.8283-0.50862.2492-0.0497-0.30550.05880.13670.01570.1342-0.0429-0.29310.0339-0.0210.03430.0026-0.0053-0.0045-0.031754.359742.556869.7696
120.80031.0643-0.19542.7827-0.00810.73030.0425-0.23950.12880.1465-0.04150.0530.0656-0.0775-0.0011-0.0292-0.01520.0114-0.05460.00090.009110.960744.298266.7681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA47 - 6527 - 45
2X-RAY DIFFRACTION2AA111 - 12491 - 104
3X-RAY DIFFRACTION3AA173 - 185153 - 165
4X-RAY DIFFRACTION4BB44 - 6524 - 45
5X-RAY DIFFRACTION5BB111 - 12491 - 104
6X-RAY DIFFRACTION6BB173 - 185153 - 165
7X-RAY DIFFRACTION7AA130 - 142110 - 122
8X-RAY DIFFRACTION7AA162 - 166142 - 146
9X-RAY DIFFRACTION7AA203 - 214183 - 194
10X-RAY DIFFRACTION7AA313 - 321293 - 301
11X-RAY DIFFRACTION7AA354 - 365334 - 345
12X-RAY DIFFRACTION8BB130 - 142110 - 122
13X-RAY DIFFRACTION8BB162 - 166142 - 146
14X-RAY DIFFRACTION8BB203 - 214183 - 194
15X-RAY DIFFRACTION8BB313 - 321293 - 301
16X-RAY DIFFRACTION8BB354 - 365334 - 345
17X-RAY DIFFRACTION9AA71 - 7451 - 54
18X-RAY DIFFRACTION9AA251 - 254231 - 234
19X-RAY DIFFRACTION9AA259 - 265239 - 245
20X-RAY DIFFRACTION9AA269 - 276249 - 256
21X-RAY DIFFRACTION9AA396 - 402376 - 382
22X-RAY DIFFRACTION9AA408 - 414388 - 394
23X-RAY DIFFRACTION10BB71 - 7451 - 54
24X-RAY DIFFRACTION10BB251 - 254231 - 234
25X-RAY DIFFRACTION10BB259 - 265239 - 245
26X-RAY DIFFRACTION10BB269 - 276249 - 256
27X-RAY DIFFRACTION10BB396 - 402376 - 382
28X-RAY DIFFRACTION10BB408 - 414388 - 394
29X-RAY DIFFRACTION11AA225 - 230205 - 210
30X-RAY DIFFRACTION11AA236 - 249216 - 229
31X-RAY DIFFRACTION11AA302 - 312282 - 292
32X-RAY DIFFRACTION11AA388 - 392368 - 372
33X-RAY DIFFRACTION12BB225 - 230205 - 210
34X-RAY DIFFRACTION12BB236 - 249216 - 229
35X-RAY DIFFRACTION12BB302 - 312282 - 292
36X-RAY DIFFRACTION12BB388 - 392368 - 372

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