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- PDB-1nyc: Staphostatins resemble lipocalins, not cystatins in fold. -

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Basic information

Entry
Database: PDB / ID: 1nyc
TitleStaphostatins resemble lipocalins, not cystatins in fold.
Componentscysteine protease inhibitor
KeywordsHYDROLASE INHIBITOR / Staphostatin B / SspC / cysteine protease inhibitor
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / cytoplasm
Similarity search - Function
Staphostatin B / Staphostatin B / Staphostatins / beta-Barrel protease inhibitors / Staphostatin A/B / Protease inhibitor, beta-barrel domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsRzychon, M. / Filipek, R. / Sabat, A. / Kosowska, K. / Dubin, A. / Potempa, J. / Bochtler, M.
Citation
Journal: Protein Sci. / Year: 2003
Title: Staphostatins resemble lipocalins, not cystatins in fold.
Authors: Rzychon, M. / Filipek, R. / Sabat, A. / Kosowska, K. / Dubin, A. / Potempa, J. / Bochtler, M.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Identification of a novel maturation mechanism and restricted substrate specificity for the SspB cysteine protease of Staphylococcus aureus
Authors: Massimi, I. / Park, E. / Rice, K. / Mueller-Esterl, W. / Sauder, D. / McGavin, M.J.
#2: Journal: Mol.Microbiol. / Year: 2003
Title: Staphostatins: an expanding new group of proteinase inhibitors with a unique specificity for the regulation of staphopains, Staphylococcus spp. cysteine proteinases.
Authors: Rzychon, M. / Sabat, A. / Kosowska, K. / Potempa, J. / Dubin, A.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence represents the V8 strain sequence of staphostatin B. Please refer to the ...SEQUENCE The sequence represents the V8 strain sequence of staphostatin B. Please refer to the primary citation for further information concerning the sequence discrepancy.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cysteine protease inhibitor
B: cysteine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3165
Polymers26,1492
Non-polymers1673
Water4,684260
1
A: cysteine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2424
Polymers13,0751
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cysteine protease inhibitor


Theoretical massNumber of molelcules
Total (without water)13,0751
Polymers13,0751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.196, 77.049, 101.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cysteine protease inhibitor / staphostatin B


Mass: 13074.622 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: staphostatin B (sspC) / Plasmid: pGEX-5T-sspC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[pLysS] / References: UniProt: Q7A189
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, PEG 4000, glycerol, manganese chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 4.60
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
25 mMTris1droppH7.5
3160 mMammonium sulfate1reservoir
480 mMsodium acetate1reservoirpH4.6
520 %PEG40001reservoir
620 %glycerol1reservoir
710 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.4→10 Å / Num. obs: 75079 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 5.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.188 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. obs: 50616 / % possible obs: 99 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22552 2661 5 %RANDOM
Rwork0.201 ---
obs0.20225 50616 99.63 %-
all-75880 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.637 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2--1.19 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 7 260 2111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211872
X-RAY DIFFRACTIONr_bond_other_d00.021602
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9112534
X-RAY DIFFRACTIONr_angle_other_deg3.77233740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022070
X-RAY DIFFRACTIONr_gen_planes_other0.010.02384
X-RAY DIFFRACTIONr_nbd_refined0.2330.2334
X-RAY DIFFRACTIONr_nbd_other0.2980.21806
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1160.2954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1861.51090
X-RAY DIFFRACTIONr_mcangle_it2.35321778
X-RAY DIFFRACTIONr_scbond_it3.483782
X-RAY DIFFRACTIONr_scangle_it5.8464.5756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 197
Rwork0.317 3632
Refinement
*PLUS
Highest resolution: 1.4 Å / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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