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- PDB-4n6v: Partial rotational order disorder structure of human stefin B -

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Basic information

Entry
Database: PDB / ID: 4n6v
TitlePartial rotational order disorder structure of human stefin B
ComponentsCystatin-B
KeywordsHYDROLASE INHIBITOR / stefin B / cystatin B / partial rotational order disorder / crystal disorder
Function / homology
Function and homology information


negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / adult locomotory behavior / negative regulation of proteolysis / tertiary granule lumen / protease binding / collagen-containing extracellular matrix / secretory granule lumen / ficolin-1-rich granule lumen ...negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / adult locomotory behavior / negative regulation of proteolysis / tertiary granule lumen / protease binding / collagen-containing extracellular matrix / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / nucleolus / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRenko, M. / Taler-Vercic, A. / Mihelic, M. / Zerovnik, E. / Turk, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Partial rotational lattice order-disorder in stefin B crystals.
Authors: Renko, M. / Taler-Vercic, A. / Mihelic, M. / Zerovnik, E. / Turk, D.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
2: Cystatin-B
1: Cystatin-B
9: Cystatin-B
8: Cystatin-B
7: Cystatin-B
6: Cystatin-B
4: Cystatin-B
3: Cystatin-B
0: Cystatin-B
5: Cystatin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,16114
Polymers104,77710
Non-polymers3844
Water13,601755
1
2: Cystatin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5742
Polymers10,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
1: Cystatin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5742
Polymers10,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
9: Cystatin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5742
Polymers10,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
8: Cystatin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5742
Polymers10,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
7: Cystatin-B


Theoretical massNumber of molelcules
Total (without water)10,4781
Polymers10,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
6: Cystatin-B


Theoretical massNumber of molelcules
Total (without water)10,4781
Polymers10,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
4: Cystatin-B


Theoretical massNumber of molelcules
Total (without water)10,4781
Polymers10,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
3: Cystatin-B


Theoretical massNumber of molelcules
Total (without water)10,4781
Polymers10,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
0: Cystatin-B


Theoretical massNumber of molelcules
Total (without water)10,4781
Polymers10,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
5: Cystatin-B


Theoretical massNumber of molelcules
Total (without water)10,4781
Polymers10,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.559, 95.559, 254.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Cystatin-B / Stefin-B / CPI-B / Liver thiol proteinase inhibitor


Mass: 10477.718 Da / Num. of mol.: 10 / Fragment: UNP residues 8-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTB / Production host: Escherichia coli (E. coli) / References: UniProt: P04080
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.06717 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06717 Å / Relative weight: 1
ReflectionNumber: 1462171 / Rmerge(I) obs: 0.069 / D res high: 1.8 Å / Num. obs: 95273 / % possible obs: 90.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.81.91986258.310.61
1.912.041403387.810.373
2.042.21452198.210.228
2.22.411350298.510.147
2.412.71219998.910.103
2.73.111081399.210.059
3.113.81922199.510.037
3.815.37713399.710.028
ReflectionResolution: 1.8→50 Å / Num. all: 105058 / Num. obs: 95273 / % possible obs: 90.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 4.7 / Num. unique all: 16923 / % possible all: 58.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1STF

1stf


Resolution: 1.8→46.37 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1893 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8597 / SU B: 5.225 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1589 / SU Rfree: 0.1465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 4751 5 %RANDOM
Rwork0.1899 ---
all0.2011 105058 --
obs0.1921 95273 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.69 Å2 / Biso mean: 23.8521 Å2 / Biso min: 8.51 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7420 0 20 755 8195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199425
X-RAY DIFFRACTIONr_bond_other_d0.0010.028910
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.93212810
X-RAY DIFFRACTIONr_angle_other_deg0.771320558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96151144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30225.041492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39151630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5571530
X-RAY DIFFRACTIONr_chiral_restr0.0970.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022304
X-RAY DIFFRACTIONr_mcbond_it1.5321.5854474
X-RAY DIFFRACTIONr_mcbond_other1.5321.5844472
X-RAY DIFFRACTIONr_mcangle_it2.5372.3685592
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 187 -
Rwork0.273 3875 -
all-4062 -
obs--52.41 %
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)
11.3663-0.12110.63240.09820.18191.1505-0.01490.0506-0.02760.00390.00110.0074-0.12740.03620.01390.08160.0052-0.0010.02560.01070.0114-0.114220.847749.836
24.11431.1860.94320.69050.52070.4201-0.0990.0263-0.0353-0.03780.06980.0016-0.03880.01970.02920.02680.01310.00520.0438-0.02450.0375-8.193519.072325.015
30.76320.99120.46913.54260.86570.33630.0983-0.0420.01370.0577-0.1269-0.02920.0273-0.04630.02860.04570.0173-0.02220.0321-00.0382-19.04798.1209-25.0581
40.2309-0.18150.21241.11340.53911.11930.00270.0168-0.00530.0364-0.0217-0.02610.0255-0.12620.0190.02810.00360.0070.0715-0.00490.0127-20.88030.0508-49.8049
50.55550.10530.11460.35860.0730.6797-0.0008-0.00360.03420.0065-0.00120.01950.04760.07640.0020.03340.0196-0.00060.06760.00830.0143-27.431643.389252.7812
60.6585-0.11980.09460.73320.00950.23490.01620.00270.0128-0.0408-0.00760.04090.03640.0462-0.00860.04290.02490.01090.0379-0.01820.0354-34.600731.77928.0457
70.74520.006-0.0290.65590.06480.1697-0.0105-0.05990.0496-0.02140.02320.01890.05920.0553-0.01270.04170.0306-0.01870.04560.00390.0358-31.800134.5596-27.9845
80.41560.1144-0.05740.4930.13270.82610.00040.01240.0240.00560.00570.02350.08110.0511-0.00610.06550.01830.01170.0345-0.00010.0128-43.392727.4199-52.7215
90.36660.04260.12681.9409-0.41260.41980.0079-0.036-0.0035-0.02120.12460.00230.004-0.1648-0.13250.0034-0.00670.0030.07950.05480.0602-20.3378-0.7454-0.0129
101.2871-0.05330.66870.06230.05170.51190.08890.0233-0.00180.0661-0.0032-0.02580.187-0.0011-0.08570.1441-0.0082-0.05030.01620.01220.0544-47.993329.4047-0.0354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION128 - 98
2X-RAY DIFFRACTION218 - 98
3X-RAY DIFFRACTION398 - 98
4X-RAY DIFFRACTION488 - 98
5X-RAY DIFFRACTION578 - 98
6X-RAY DIFFRACTION668 - 98
7X-RAY DIFFRACTION748 - 98
8X-RAY DIFFRACTION838 - 98
9X-RAY DIFFRACTION908 - 98
10X-RAY DIFFRACTION1058 - 98

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