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- PDB-5kd5: BT_4244 metallopeptidase from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 5kd5
TitleBT_4244 metallopeptidase from Bacteroides thetaiotaomicron
ComponentsMetallopeptidase
KeywordsHYDROLASE / O-glycopeptidase / PF13402/M60-like
Function / homology
Function and homology information


: / Peptidase M60, C-terminal / Peptidase M60 C-terminal domain / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family ...: / Peptidase M60, C-terminal / Peptidase M60 C-terminal domain / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / Peptidase M60 domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNoach, I. / Boraston, A.B.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Recognition of protein-linked glycans as a determinant of peptidase activity.
Authors: Noach, I. / Ficko-Blean, E. / Pluvinage, B. / Stuart, C. / Jenkins, M.L. / Brochu, D. / Buenbrazo, N. / Wakarchuk, W. / Burke, J.E. / Gilbert, M. / Boraston, A.B.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 27, 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: Metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6196
Polymers64,2721
Non-polymers3475
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.860, 88.440, 99.020
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 Metallopeptidase


Mass: 64272.113 Da / Num. of mol.: 1 / Fragment: UNP residues 322-857
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4244
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q89ZX7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, NaH2PO4, Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→38.68 Å / Num. obs: 92144 / % possible obs: 99.8 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KD2

5kd2


Resolution: 1.65→38.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.412 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22067 4813 5.2 %RANDOM
Rwork0.18583 ---
obs0.18763 87249 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.115 Å2
Baniso -1Baniso -2Baniso -3
1-3.16 Å20 Å20 Å2
2---2.11 Å20 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.65→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 18 606 4974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194516
X-RAY DIFFRACTIONr_bond_other_d0.0010.024129
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9326109
X-RAY DIFFRACTIONr_angle_other_deg0.87239507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05824.805231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37515770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3991517
X-RAY DIFFRACTIONr_chiral_restr0.1080.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021104
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_it2.0162.4832162
X-RAY DIFFRACTIONr_mcbond_other2.0132.4822161
X-RAY DIFFRACTIONr_mcangle_it2.6913.7182706
X-RAY DIFFRACTIONr_mcangle_other2.6923.7192707
X-RAY DIFFRACTIONr_scbond_it2.6992.722354
X-RAY DIFFRACTIONr_scbond_other2.6972.7162350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0093.9723398
X-RAY DIFFRACTIONr_long_range_B_refined5.76521.6685882
X-RAY DIFFRACTIONr_long_range_B_other5.53420.8375561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 353 -
Rwork0.259 6412 -
obs--100 %

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