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- PDB-5kdn: ZmpB metallopeptidase from Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 5kdn
TitleZmpB metallopeptidase from Clostridium perfringens
ComponentsF5/8 type C domain proteinDiscoidin domain
KeywordsHYDROLASE / O-glycopeptidase / PF13402/M60-like
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / 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 / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
F5/8 type C domain protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsNoach, I. / Ficko-Blean, E. / Stuart, C. / 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 8, 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F5/8 type C domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4577
Polymers60,0811
Non-polymers3766
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.890, 68.020, 170.860
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 F5/8 type C domain protein / Discoidin domain / Metallopeptidase


Mass: 60080.852 Da / Num. of mol.: 1 / Fragment: UNP residues 497-1003
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: CPF_1489
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H2YN38
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, Na/K tartrate, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.66→43.09 Å / Num. obs: 92133 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.5
Reflection shellResolution: 1.66→1.68 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 5.3 / % 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: 5KDJ

5kdj


Resolution: 1.66→43.09 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.412 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18046 4594 5 %RANDOM
Rwork0.15376 ---
obs0.15508 87452 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--2.9 Å20 Å2
3----1.54 Å2
Refinement stepCycle: 1 / Resolution: 1.66→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 21 622 4706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024312
X-RAY DIFFRACTIONr_bond_other_d0.0010.024003
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9455840
X-RAY DIFFRACTIONr_angle_other_deg0.89839247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88625.205219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11315749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3011519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021021
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_it1.782.0012101
X-RAY DIFFRACTIONr_mcbond_other1.77622100
X-RAY DIFFRACTIONr_mcangle_it2.6122.9982649
X-RAY DIFFRACTIONr_mcangle_other2.6132.9992650
X-RAY DIFFRACTIONr_scbond_it3.022.2752211
X-RAY DIFFRACTIONr_scbond_other3.0172.2752211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5693.2763192
X-RAY DIFFRACTIONr_long_range_B_refined6.28217.9255597
X-RAY DIFFRACTIONr_long_range_B_other6.28117.9285598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.656→1.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 351 -
Rwork0.194 6391 -
obs--99.99 %

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