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- PDB-6cxd: Crystal structure of peptidase B from Yersinia pestis CO92 at 2.7... -

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Basic information

Entry
Database: PDB / ID: 6cxd
TitleCrystal structure of peptidase B from Yersinia pestis CO92 at 2.75 A resolution
ComponentsPeptidase B
KeywordsHYDROLASE / peptidase B / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


PepB aminopeptidase / metalloaminopeptidase activity / peptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, peptidase B / : / Peptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain
Similarity search - Domain/homology
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWoinska, M. / Lipowska, J. / Shabalin, I.G. / Cymborowski, M. / Grimshaw, S. / Winsor, J. / Shuvalova, L. / Satchell, K.J. / Joachimiak, A. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Febs J. / Year: 2020
Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D.
History
DepositionApr 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 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: Peptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9007
Polymers49,3231
Non-polymers5766
Water59433
1
A: Peptidase B
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)299,39842
Polymers295,9406
Non-polymers3,45836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area25550 Å2
ΔGint-667 kcal/mol
Surface area88810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.558, 101.558, 240.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-505-

SO4

21A-505-

SO4

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Components

#1: Protein Peptidase B / Aminopeptidase B


Mass: 49323.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: pepB, YPO2889, y1342, YP_2566 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P58475, PepB aminopeptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 uL 14 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 1 mM ZnCl2 + 0.2 uL TOP96 #29 (0.2 M ammonium sulfate, 0.1 M sodium ...Details: 0.2 uL 14 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 1 mM ZnCl2 + 0.2 uL TOP96 #29 (0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% w/v PEG8000) against 1.5 M sodium chloride, 96-well 3-drop crystallization plate (Swissci)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 12769 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/av σ(I): 16.5 / Net I/σ(I): 16.5
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 600 / CC1/2: 0.928 / Rsym value: 0.666 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-3000v716.4data reduction
DENZOdata reduction
HKL-3000v716.4data scaling
SCALEPACKdata scaling
HKL-3000v716.4phasing
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IJ3

3ij3


Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 29.699 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24925 600 4.8 %RANDOM
Rwork0.17761 ---
obs0.18097 11976 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.74 Å2
Refinement stepCycle: 1 / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 30 33 3226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193244
X-RAY DIFFRACTIONr_bond_other_d0.0010.022957
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.9554403
X-RAY DIFFRACTIONr_angle_other_deg0.72836839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.70624.552145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09915522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7561520
X-RAY DIFFRACTIONr_chiral_restr0.0580.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4783.4431669
X-RAY DIFFRACTIONr_mcbond_other3.4643.4411668
X-RAY DIFFRACTIONr_mcangle_it5.2775.1522081
X-RAY DIFFRACTIONr_mcangle_other5.285.1542082
X-RAY DIFFRACTIONr_scbond_it4.2083.7161575
X-RAY DIFFRACTIONr_scbond_other3.7923.6441548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7465.3522285
X-RAY DIFFRACTIONr_long_range_B_refined8.31939.9473482
X-RAY DIFFRACTIONr_long_range_B_other8.32239.963483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 46 -
Rwork0.273 758 -
obs--87.3 %
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)
12.89780.42331.98510.90870.64962.244-0.02890.0253-0.03420.03580.0916-0.26020.07180.0512-0.06280.0698-0.00170.04250.07580.02770.376538.43146.46127.624
23.5669-1.07-0.19422.4912-0.2951.6472-0.02030.21320.0099-0.1360.00460.0238-0.0265-0.11220.01570.0713-0.01280.02670.1-0.02710.119610.86936.95914.537
32.3783-0.41850.79661.25010.1591.14530.172-0.0865-0.1346-0.0151-0.064-0.10.1175-0.1037-0.10810.0406-0.00630.0460.0140.0260.170512.53130.85931.833
44.55142.16041.17613.02950.45821.20990.0901-0.16250.0560.1837-0.10950.16750.0361-0.07110.01930.10940.01290.05270.06410.02330.175217.0334.18727.32
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 141
2X-RAY DIFFRACTION2A142 - 312
3X-RAY DIFFRACTION3A313 - 367
4X-RAY DIFFRACTION4A368 - 432

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