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- PDB-6thj: CBDP35 Native structure -

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Basic information

Entry
Database: PDB / ID: 6thj
TitleCBDP35 Native structure
ComponentsPlyP35
KeywordsHYDROLASE
Function / homologyPSA endolysin, cell wall binding domain / PSA endolysin C-terminal cell wall binding domain / Peptidase M15C / D-alanyl-D-alanine carboxypeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / peptidase activity / PlyP35
Function and homology information
Biological speciesListeria phage P35 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHermoso, J.A. / Bartual, S.G.
CitationJournal: To Be Published
Title: CBDP35 Native structure
Authors: Hermoso, J.A. / Bartual, S.G.
History
DepositionNov 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: PlyP35
B: PlyP35
C: PlyP35
D: PlyP35
E: PlyP35
F: PlyP35
G: PlyP35
H: PlyP35
I: PlyP35
J: PlyP35
K: PlyP35
L: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,73233
Polymers193,08612
Non-polymers4,64521
Water23,2031288
1
A: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3122
Polymers16,0911
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5333
Polymers16,0911
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3122
Polymers16,0911
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: PlyP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3122
Polymers16,0911
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)332.510, 94.590, 83.190
Angle α, β, γ (deg.)90.000, 90.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11J-396-

HOH

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Components

#1: Protein
PlyP35


Mass: 16090.521 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage P35 (virus) / Gene: ply / Production host: Escherichia coli (E. coli) / References: UniProt: A8ATR6
#2: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 298.5 K / Method: vapor diffusion / Details: 4M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.2→37.88 Å / Num. obs: 130198 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6370 / CC1/2: 0.686 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S3Y

6s3y


Resolution: 2.2→37.88 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.019 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 6428 4.9 %RANDOM
Rwork0.1962 ---
obs0.1983 123766 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.22 Å2 / Biso mean: 31.326 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å21.03 Å2
2--1.5 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 2.2→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13570 0 315 1288 15173
Biso mean--42.54 35.96 -
Num. residues----1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01314297
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713082
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.67419225
X-RAY DIFFRACTIONr_angle_other_deg1.2631.62230429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33951654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51322.197710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.759152514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7341560
X-RAY DIFFRACTIONr_chiral_restr0.070.21829
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215569
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023240
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 474 -
Rwork0.298 9080 -
all-9554 -
obs--99.08 %

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