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- PDB-4nv4: 1.8 Angstrom Crystal Structure of Signal Peptidase I from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4nv4
Title1.8 Angstrom Crystal Structure of Signal Peptidase I from Bacillus anthracis.
ComponentsSignal peptidase I
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


signal peptidase I / protein secretion / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A ...Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Signal peptidase / Signal peptidase I
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.8 Angstrom Crystal Structure of Signal Peptidase I from Bacillus anthracis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal peptidase I
B: Signal peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4299
Polymers40,5102
Non-polymers9197
Water3,711206
1
A: Signal peptidase I
hetero molecules

A: Signal peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2348
Polymers40,5102
Non-polymers7256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area5220 Å2
ΔGint-23 kcal/mol
Surface area14700 Å2
MethodPISA
2
B: Signal peptidase I
hetero molecules

B: Signal peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,62310
Polymers40,5102
Non-polymers1,1138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area5800 Å2
ΔGint-2 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.225, 80.225, 174.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsChain A and the symmetry related to it chain A, and chain B and the symmetry related to it chain B form dimers.

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Components

#1: Protein Signal peptidase I /


Mass: 20254.785 Da / Num. of mol.: 2 / Fragment: Signal Peptidase I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS1059, BA_1140, GBAA_1140, sipT / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: Q81TW3, UniProt: A0A6L7HM74*PLUS, signal peptidase I
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.3 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 31574 / Num. obs: 31574 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 30
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1542 / Rsym value: 0.512 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ME8

4me8


Resolution: 1.8→29.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.001 / SU ML: 0.064
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 1591 5 %RANDOM
Rwork0.17272 ---
all0.17403 29946 --
obs0.17403 29946 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å2-0 Å2
2--0.56 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 61 206 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192090
X-RAY DIFFRACTIONr_bond_other_d0.0010.022017
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.972805
X-RAY DIFFRACTIONr_angle_other_deg0.73634670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4545250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.51424.206107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4915370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0771512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
X-RAY DIFFRACTIONr_mcbond_it1.882.001970
X-RAY DIFFRACTIONr_mcbond_other1.871.998969
X-RAY DIFFRACTIONr_mcangle_it2.8492.9811230
X-RAY DIFFRACTIONr_mcangle_other2.852.9841231
X-RAY DIFFRACTIONr_scbond_it3.0072.5291119
X-RAY DIFFRACTIONr_scbond_other3.0012.5291119
X-RAY DIFFRACTIONr_scangle_other4.6283.581575
X-RAY DIFFRACTIONr_long_range_B_refined7.60918.0242435
X-RAY DIFFRACTIONr_long_range_B_other7.51417.3612361
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 125 -
Rwork0.214 2130 -
obs-2130 99.91 %
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)
11.85170.1520.7767.4463-3.03311.17960.0985-0.1318-0.15620.09990.08130.37160.1066-0.9035-0.17980.02120.0080.00740.120.01770.082624.579585.1526-8.2611
21.7365-0.07660.15551.7065-0.27363.6530.0582-0.0912-0.0081-0.0873-0.0943-0.12810.19760.21360.0360.0262-0.01190.00730.07470.0160.117332.907551.253617.5078
35.0223-0.8743-1.15352.26580.06233.23070.2014-0.1360.31160.1219-0.1836-0.2983-0.02660.3603-0.01780.0229-0.0183-0.01760.07370.03750.115738.353554.328418.8476
41.251-0.4119-0.57491.934-0.99135.12640.01830.08690.2634-0.1073-0.0797-0.0325-0.03340.00530.06140.0125-0.00240.00680.04240.02080.10830.850755.69749.7297
54.0177-4.3268-2.41777.88412.55334.72560.01790.13870.2380.13840.0744-0.22270.06660.1119-0.09230.0263-0.0061-0.00590.0981-0.01160.06374.478765.7850.6448
61.76151.29871.49872.99411.08621.9368-0.08920.1769-0.1551-0.10740.1398-0.0970.12740.0456-0.05060.0936-0.06020.02480.0502-0.01260.077915.046833.994925.7282
73.2762.43240.86093.23170.60811.66970.01980.0645-0.0272-0.089-0.0003-0.01050.167-0.0593-0.01950.0933-0.05190.01490.0399-0.0120.050111.184632.984426.0111
82.17150.48570.28692.4515-0.76294.9241-0.0213-0.01520.14940.0756-0.06370.02930.03970.22230.0850.0768-0.04230.02760.0399-0.02540.05617.224539.221135.2105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 75
2X-RAY DIFFRACTION2A76 - 108
3X-RAY DIFFRACTION3A109 - 140
4X-RAY DIFFRACTION4A141 - 173
5X-RAY DIFFRACTION5B62 - 76
6X-RAY DIFFRACTION6B77 - 102
7X-RAY DIFFRACTION7B103 - 150
8X-RAY DIFFRACTION8B151 - 173

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