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- PDB-3erv: Crystal structure of an putative C39-like peptidase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 3erv
TitleCrystal structure of an putative C39-like peptidase from Bacillus anthracis
Componentsputative C39-like peptidase
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Uncharacterised conserved protein UCP032442 / Peptidase C39 single domain protein / Peptidase C39-like / Peptidase_C39 like family / Cysteine proteinases / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptidase C39-like domain-containing protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Iizuka, M. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an putative C39-like peptidase from Bacillus anthracis
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Iizuka, M. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative C39-like peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9273
Polymers26,8031
Non-polymers1242
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.167, 117.167, 36.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein putative C39-like peptidase


Mass: 26803.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BA_0574, GBAA0574 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VC3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 10% ethylene glycol, pH 7.0, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.1→33.826 Å / Num. all: 17110 / Num. obs: 17110 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.3 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 4.2 / Num. measured all: 49803 / Num. unique all: 2473 / Rsym value: 0.523 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.298 / WRfactor Rwork: 0.252 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.705 / SU B: 5.627 / SU ML: 0.145 / SU R Cruickshank DPI: 0.201 / SU Rfree: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.201 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 874 5.1 %RANDOM
Rwork0.226 ---
obs0.228 17073 100 %-
all-17073 --
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: 90.94 Å2 / Biso mean: 53.316 Å2 / Biso min: 30.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 8 94 1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221598
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9672164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.70425.77571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.04154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211200
X-RAY DIFFRACTIONr_mcbond_it0.9421.5994
X-RAY DIFFRACTIONr_mcangle_it1.74821608
X-RAY DIFFRACTIONr_scbond_it2.8533604
X-RAY DIFFRACTIONr_scangle_it4.5714.5556
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 75 -
Rwork0.463 1192 -
all-1267 -
obs-1192 100 %

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