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- PDB-3l0r: Crystal Structure of Salivary Cystatin from the Soft Tick Ornitho... -

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Basic information

Entry
Database: PDB / ID: 3l0r
TitleCrystal Structure of Salivary Cystatin from the Soft Tick Ornithodoros moubata
ComponentsCystatin-2
KeywordsHYDROLASE INHIBITOR / soft tick / cystatin / Protease inhibitor / Thiol protease inhibitor
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesOrnithodoros moubata (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRezacova, P. / Brynda, J. / Andersen, J.F. / Salat, J. / Kovarova, Z. / Mares, M.
CitationJournal: Biochem.J. / Year: 2010
Title: Crystal structure and functional characterization of an immunomodulatory salivary cystatin from the soft tick Ornithodoros moubata
Authors: Salat, J. / Paesen, G.C. / Rezacova, P. / Kotsyfakis, M. / Kovarova, Z. / Sanda, M. / Majtan, J. / Grunclova, L. / Horka, H. / Andersen, J.F. / Brynda, J. / Horn, M. / Nunn, M.A. / Kopacek, ...Authors: Salat, J. / Paesen, G.C. / Rezacova, P. / Kotsyfakis, M. / Kovarova, Z. / Sanda, M. / Majtan, J. / Grunclova, L. / Horka, H. / Andersen, J.F. / Brynda, J. / Horn, M. / Nunn, M.A. / Kopacek, P. / Kopecky, J. / Mares, M.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystatin-2
B: Cystatin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5007
Polymers26,1532
Non-polymers3475
Water2,018112
1
A: Cystatin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2043
Polymers13,0771
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cystatin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2964
Polymers13,0771
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.805, 69.805, 133.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 3 - 107 / Label seq-ID: 3 - 107

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cystatin-2 / / OmC2


Mass: 13076.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithodoros moubata (arthropod) / Gene: OmC2 / Plasmid: pBacPAK9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6QD55
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.5M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 14369 / % possible obs: 98.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 53.4 Å2 / Rsym value: 0.057 / Net I/σ(I): 27.3
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1285 / % possible all: 90

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LH4

3lh4


Resolution: 2.45→30.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.071 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22312 744 5.2 %RANDOM
Rwork0.1875 ---
obs0.18937 13588 98.86 %-
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 max: 106.15 Å2 / Biso mean: 39.921 Å2 / Biso min: 30.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.52 Å20 Å2
2---1.03 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 20 112 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9422447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6822584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68715305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.203159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2721
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21185
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0420.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4711.51123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79621795
X-RAY DIFFRACTIONr_scbond_it1.3163767
X-RAY DIFFRACTIONr_scangle_it2.0534.5646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 793 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.370.5
medium thermal0.522
LS refinement shellResolution: 2.448→2.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 39 -
Rwork0.262 899 -
obs-899 88.57 %
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)
112.74512.9644-16.018815.4315-11.660329.7041-0.5918-0.66450.41910.8912-1.1558-1.6898-0.15564.00861.74770.43970.0495-0.04990.89120.00770.0834-6.17521.431-27.87
29.63451.2795-0.02722.88010.5713.3665-0.0907-0.1986-0.8408-0.0031-0.1088-0.1180.33780.19270.19950.2839-0.00380.02090.22870.026-0.003-17.9715.166-39.167
36.41831.5277-2.56923.1656-0.19315.132-0.13670.2503-0.09670.2638-0.13740.3642-0.0041-0.25570.27410.2181-0.0498-0.00390.3248-0.04090.0785-34.63120.789-39.607
44.37340.41274.28052.0752-1.988321.06750.07340.02520.11340.0210.045-0.1007-0.7920.8042-0.11830.20110.00150.0450.22880.0040.008-14.12320.519-34.16
57.86860.03133.75992.5483-0.10073.95880.0104-0.0764-0.4595-0.1321-0.00430.29320.3074-0.3366-0.00610.278-0.0530.02320.3053-0.0940.0134-31.52116.441-40.471
64.33230.5239-1.08214.629-0.00240.2739-0.26630.58930.3362-0.44340.01560.2803-0.4357-0.15490.25070.261-0.0602-0.01020.4334-0.0506-0.0049-27.40823.051-43.32
77.64565.34144.77547.1563-4.416528.6555-0.07950.4856-0.5939-0.08840.25910.47630.7097-0.3882-0.17970.3016-0.03740.09380.29060.01260.0885-20.11810.702-22.808
88.9758-3.49395.92321.0711-7.65421.8131-0.23190.01480.7143-0.0293-0.1548-0.245-0.5309-0.23180.38670.0766-0.01680.03580.3546-0.1236-0.0038-25.37325.083-33.678
915.9012.8809-5.36829.3442-7.743312.2037-0.066-0.2809-0.9102-0.0432-0.4804-2.1220.09671.30840.54630.290.0154-0.02910.4648-0.04510.35067.96417.931-11.567
1013.21660.0084-3.32075.3099-1.69844.9238-0.2703-1.6687-0.16370.56960.0515-0.5221-0.29450.55840.21890.29310.0248-0.03160.39830.03960.0251-6.65514.896-6.007
115.18810.8423-2.336210.97321.04295.1348-0.29030.3122-0.2023-0.27110.16230.48050.3415-0.47260.1280.1794-0.00120.02850.26170.00770.0479-18.73213.68-14.221
124.3455-0.6296-2.0127.7069-1.94341.5875-0.327-0.1702-0.7114-0.45470.2966-0.75310.22040.64790.03040.3280.0626-0.02330.3993-0.0030.08212.18917.638-11.794
134.48131.2572-1.30683.71530.60534.8498-0.2863-0.2007-0.74630.12610.1212-0.03680.2774-0.04290.16510.20160.06830.01930.17660.06480.0407-13.14613.722-11.39
149.9652-0.1599-4.06626.58953.37915.0081-0.3904-0.4787-1.38070.52030.00630.19420.9268-0.07240.38410.37410.10410.09830.22690.12780.2365-17.166.927-9.24
154.35094.21542.225412.18218.53847.4304-0.0083-0.48020.27370.3208-0.09930.3440.0826-0.11550.10750.26380.05810.02460.3018-0.05960.0446-4.00426.497-7.106
1612.64487.52252.338217.86964.606910.5697-0.65011.1795-0.4939-0.77370.6045-0.47010.09690.36240.04560.1647-0.01690.06210.2986-0.01470.0048-8.39218.288-19.821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 40
4X-RAY DIFFRACTION4A41 - 51
5X-RAY DIFFRACTION5A52 - 78
6X-RAY DIFFRACTION6A79 - 93
7X-RAY DIFFRACTION7A94 - 100
8X-RAY DIFFRACTION8A101 - 110
9X-RAY DIFFRACTION9B3 - 11
10X-RAY DIFFRACTION10B12 - 27
11X-RAY DIFFRACTION11B28 - 40
12X-RAY DIFFRACTION12B41 - 51
13X-RAY DIFFRACTION13B52 - 70
14X-RAY DIFFRACTION14B71 - 87
15X-RAY DIFFRACTION15B88 - 101
16X-RAY DIFFRACTION16B102 - 110

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