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- PDB-8z4f: Pseudomurein Endoisopeptidases PeiP -

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Basic information

Entry
Database: PDB / ID: 8z4f
TitlePseudomurein Endoisopeptidases PeiP
ComponentsPseudomurein endosiopeptidase
KeywordsLYASE / Pseudomurein Endoisopeptidases from Methanogenic Archaea
Function / homologyPseudomurein-binding repeat / Peptidase C71, pseudomurein endo-isopeptidase Pei / Pseudomurein-binding repeat / Pseudomurein endo-isopeptidase Pei / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Pseudomurein endoisopeptidase
Function and homology information
Biological speciesMethanobacterium phage psiM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGuo, L. / Bai, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)42203080 China
National Natural Science Foundation of China (NSFC)31970066 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Insights into the catalytic mechanism of archaeal peptidoglycan endoisopeptidases from methanogenic phages.
Authors: Guo, L. / Zhu, Y. / Zhao, N. / Leng, H. / Wang, S. / Yang, Q. / Zhao, P. / Chen, Y. / Cha, G. / Bai, L. / Bao, R.
History
DepositionApr 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Pseudomurein endosiopeptidase
A: Pseudomurein endosiopeptidase


Theoretical massNumber of molelcules
Total (without water)71,1142
Polymers71,1142
Non-polymers00
Water4,684260
1
A: Pseudomurein endosiopeptidase

B: Pseudomurein endosiopeptidase


Theoretical massNumber of molelcules
Total (without water)71,1142
Polymers71,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_454x-1/2,-y+1/2,-z-1/21
Buried area4590 Å2
ΔGint-12 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.340, 113.100, 120.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Pseudomurein endosiopeptidase


Mass: 35556.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobacterium phage psiM2 (virus) / Gene: peiP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q77WJ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Precipitant:1.00 M Ammonium sulfate; Buffer:100 mM Sodium acetate; pH 4.6;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.88→37.64 Å / Num. obs: 54666 / % possible obs: 92.79 % / Redundancy: 3.3 % / CC1/2: 1 / Rrim(I) all: 0.028 / Net I/σ(I): 22.13
Reflection shellResolution: 1.88→1.947 Å / Num. unique obs: 54666 / CC1/2: 0.637

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→37.64 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1991 3.64 %
Rwork0.1961 --
obs0.1974 54654 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 0 260 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014384
X-RAY DIFFRACTIONf_angle_d1.1415933
X-RAY DIFFRACTIONf_dihedral_angle_d6.362601
X-RAY DIFFRACTIONf_chiral_restr0.069620
X-RAY DIFFRACTIONf_plane_restr0.011773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.3694970.312493X-RAY DIFFRACTION62
1.93-1.980.26541020.25052752X-RAY DIFFRACTION69
1.98-2.040.30611180.23173149X-RAY DIFFRACTION79
2.04-2.10.25451410.21843587X-RAY DIFFRACTION90
2.1-2.180.24431480.20464021X-RAY DIFFRACTION99
2.18-2.270.26671570.20683993X-RAY DIFFRACTION100
2.27-2.370.21631390.19794039X-RAY DIFFRACTION100
2.37-2.490.25771570.20524024X-RAY DIFFRACTION100
2.49-2.650.26551540.19914036X-RAY DIFFRACTION100
2.65-2.850.2621450.19684063X-RAY DIFFRACTION100
2.85-3.140.21461660.20274044X-RAY DIFFRACTION100
3.14-3.60.23261530.1844079X-RAY DIFFRACTION100
3.6-4.530.18041570.17174125X-RAY DIFFRACTION100
4.53-37.640.23551570.19894258X-RAY DIFFRACTION100

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