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- PDB-5c98: 1.45A resolution structure of SRPN18 from Anopheles gambiae -

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Basic information

Entry
Database: PDB / ID: 5c98
Title1.45A resolution structure of SRPN18 from Anopheles gambiae
ComponentsAGAP007691-PB
KeywordsUNKNOWN FUNCTION / serpin / serine protease / insect immunity / enzyme inhibitor
Function / homology
Function and homology information


negative regulation of endopeptidase activity / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Leukocyte elastase inhibitor (serpin B1) / 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 ...Leukocyte elastase inhibitor (serpin B1) / 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
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsLovell, S. / Battaile, K.P. / Gulley, M. / Zhang, X. / Meekins, D.A. / Gao, F.P. / Michel, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI095842 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: 1.45 angstrom resolution structure of SRPN18 from the malaria vector Anopheles gambiae.
Authors: Meekins, D.A. / Zhang, X. / Battaile, K.P. / Lovell, S. / Michel, K.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _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: AGAP007691-PB
B: AGAP007691-PB


Theoretical massNumber of molelcules
Total (without water)86,3572
Polymers86,3572
Non-polymers00
Water9,674537
1
A: AGAP007691-PB


Theoretical massNumber of molelcules
Total (without water)43,1791
Polymers43,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGAP007691-PB


Theoretical massNumber of molelcules
Total (without water)43,1791
Polymers43,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.419, 87.485, 194.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGAP007691-PB


Mass: 43178.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: SRPN18, AgaP_AGAP007691 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRare / References: UniProt: A7UR55
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 100 mM Bis-Tris, 200 mM NaCl, 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→48.7 Å / Num. obs: 122919 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Net I/σ(I): 20.1 / Num. measured all: 808528 / Scaling rejects: 61
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 98.9

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
1.45-1.476.70.8412.53987959360.7460.346
7.94-48.760.02656.553278830.9990.011

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.36 Å
Translation2.5 Å29.36 Å

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZF

3pzf


Resolution: 1.45→36.692 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 6160 5.02 %
Rwork0.1652 116670 -
obs0.1661 122830 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.43 Å2 / Biso mean: 24.9911 Å2 / Biso min: 10.69 Å2
Refinement stepCycle: final / Resolution: 1.45→36.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5709 0 0 537 6246
Biso mean---32 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085927
X-RAY DIFFRACTIONf_angle_d0.9748079
X-RAY DIFFRACTIONf_chiral_restr0.074913
X-RAY DIFFRACTIONf_plane_restr0.0071063
X-RAY DIFFRACTIONf_dihedral_angle_d13.6862164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.30412110.26993743395499
1.4665-1.48370.30612030.25713857406099
1.4837-1.50180.23171980.24383831402999
1.5018-1.52080.26571940.22433790398499
1.5208-1.54090.2512160.20473854407099
1.5409-1.5620.21942060.20173855406199
1.562-1.58430.23292070.19413793400099
1.5843-1.60790.21691830.18943886406999
1.6079-1.63310.21342070.18043825403299
1.6331-1.65980.20322210.17643831405299
1.6598-1.68840.18251960.169938944090100
1.6884-1.71910.2141970.174638304027100
1.7191-1.75220.21562220.179838954117100
1.7522-1.7880.22451920.17438084000100
1.788-1.82690.21442090.16839104119100
1.8269-1.86930.19952080.17238374045100
1.8693-1.91610.20322060.168638994105100
1.9161-1.96790.17772150.163938464061100
1.9679-2.02580.18191970.157139174114100
2.0258-2.09120.2021920.155539054097100
2.0912-2.16590.18692230.157238604083100
2.1659-2.25260.16311910.156839264117100
2.2526-2.35510.1812290.155738624091100
2.3551-2.47930.16841930.155739304123100
2.4793-2.63460.1851970.161439164113100
2.6346-2.83790.18762060.171939674173100
2.8379-3.12340.17921950.18239864181100
3.1234-3.5750.19222110.16553971418299
3.575-4.50280.15052390.13693997423699
4.5028-36.7040.17281960.16224249444599
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)
10.9076-0.13-0.0150.39920.44940.49390.01970.0262-0.13540.16110.0230.1301-0.0195-0.14950.00010.1432-0.0483-0.01510.1860.02180.169436.71068.724128.4867
20.53-0.25630.03280.91430.90621.06060.0876-0.05080.00090.0361-0.12990.0812-0.0929-0.1863-0.00030.132-0.0336-0.00020.1914-0.00760.1534.948916.484534.9302
31.03450.28490.28690.32770.30651.5730.097-0.0997-0.12970.15180.0207-0.1240.09970.15680.00610.1808-0.0234-0.00130.19620.01040.150545.59415.092542.0713
41.29850.0424-0.33480.9606-0.08850.70270.1222-0.15630.17520.0316-0.007-0.1266-0.24250.169700.2711-0.0650.01830.2081-0.02130.16644.830830.151944.5677
50.64730.4822-0.20780.63620.32830.54010.13710.19440.3529-0.24470.0686-0.2552-0.4448-0.01070.00430.3651-0.01040.0610.28230.01130.280645.535433.154932.6514
60.5999-0.1929-0.80950.77460.5771.88480.0491-0.13920.0413-0.04610.2159-0.243-0.09370.40190.1650.0013-0.0078-0.01010.1662-0.04650.118756.143711.126115.9865
70.60120.106-0.80710.89710.42841.3657-0.00430.0978-0.17060.0320.0521-0.07680.22570.0962-00.13940.0047-0.01960.1646-0.00550.146748.54213.700116.7078
80.2208-0.02030.11710.45140.46960.5571-0.03370.1336-0.1662-0.01540.01970.03340.3083-0.2430.00080.1535-0.0426-0.00260.16530.00150.193138.732.716317.3723
90.61330.0635-1.10280.21560.46752.53050.1527-0.0690.0436-0.0981-0.044-0.0772-0.20420.04160.00130.1174-0.0176-0.02470.18830.01210.15745.086514.404522.2602
100.1710.13810.33390.8190.17771.22380.1816-0.01640.0133-0.0134-0.1220.02-0.369-0.15950.00690.2213-0.02830.0260.1791-0.00190.115836.297227.201839.0394
110.6963-0.101-0.62351.3798-0.22911.27150.0664-0.2192-0.03430.00910.0817-0.28170.22370.25070.02120.11690.0123-0.02580.1847-0.0190.176654.04635.52215.9984
121.4265-0.8554-0.27511.15391.23931.48820.1558-0.02570.19820.080.106-0.1438-0.47270.10210.11940.1387-0.0611-0.00180.1366-0.03150.160850.276615.943919.9764
130.86550.33710.19151.53011.11741.2230.0055-0.00160.04770.0516-0.1010.1272-0.0325-0.172-0.00350.10770.00230.00140.1298-0.00110.157438.2229-11.9674-26.6974
141.06-0.3950.08880.98190.32630.8683-0.04260.2640.1104-0.18130.0348-0.3421-0.09350.19150.00050.15-0.0281-0.00070.17260.03610.215748.8587-12.842-35.592
151.80060.36050.27731.11030.82580.48850.04340.2333-0.15040.0091-0.0221-0.36610.24990.1766-0.00340.17560.0286-0.00360.1115-0.01750.207248.643-28.1906-37.2832
160.61740.01930.13780.58370.62060.70980.1052-0.2516-0.54370.087-0.0174-0.94070.2574-0.0015-0.03890.3165-0.0367-0.09950.23650.03220.447249.4185-30.1469-25.124
17-0.01120.2706-0.1827-0.18810.3148-0.01260.2154-0.1888-0.45710.04440.0019-0.67880.16280.0065-0.14990.1299-0.0192-0.06750.17480.01270.271556.3384-11.7402-21.5688
181.18940.9476-0.26321.09740.32691.69110.0388-0.1542-0.03590.0769-0.0146-0.17670.21160.18210.00590.20180.0232-0.02170.17090.02950.168558.1387-4.3569-3.2004
190.8051-0.27950.54521.53220.92261.1529-0.07410.00910.10130.06430.0712-0.02170.1363-0.0124-00.1911-0.008-0.02360.14460.00820.167349.9895-0.0352-10.8342
200.4699-0.27780.04430.48890.45790.6230.0417-0.0530.16280.2973-0.05360.4489-0.2038-0.26920.00010.20860.01570.0040.19320.00820.243339.95380.2812-11.9214
211.20990.70071.190.20860.85491.62690.2241-0.1363-0.04030.266-0.1615-0.06950.2328-0.08350.00130.1741-0.01490.00690.17360.01470.190647.2107-11.2196-15.8445
220.333-0.2354-0.33311.4317-0.23270.84710.1507-0.0645-0.13640.1018-0.1248-0.0050.3478-0.253-0.01320.1707-0.0104-0.00670.1356-0.00290.144840.7732-24.9426-31.375
231.16750.36650.01540.94690.54912.42370.0137-0.0225-0.00510.10610.0633-0.13730.05060.25090.01710.1260.0054-0.02370.10730.01250.145355.3745-3.4105-11.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 41 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 83 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 113 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 155 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 177 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 228 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 258 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 277 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 278 through 312 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 313 through 337 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 338 through 369 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 370 through 390 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid 23 through 83 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 113 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 114 through 155 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 156 through 177 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 178 through 195 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 196 through 228 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 229 through 258 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 259 through 277 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 278 through 312 )B0
22X-RAY DIFFRACTION22chain 'B' and (resid 313 through 338 )B0
23X-RAY DIFFRACTION23chain 'B' and (resid 339 through 388 )B0

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