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- PDB-8z4n: Pseudomurein Endoisopeptidase PeiR-C90A -

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Basic information

Entry
Database: PDB / ID: 8z4n
TitlePseudomurein Endoisopeptidase PeiR-C90A
ComponentsEndoisopeptidase PeiR
KeywordsHYDROLASE / Methanogenic archaea / pseudomurein / endopeptidases / C39 peptidase
Function / homologyPeptidase C39 family / Peptidase C39, bacteriocin processing / peptidase activity / proteolysis / ATP binding / membrane / Endoisopeptidase PeiR
Function and homology information
Biological speciesMethanobrevibacter ruminantium M1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.769 Å
AuthorsGuo, L.Z. / Wang, S.X. / Bai, L.p.
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: To Be Published
Title: Pseudomurein Endoisopeptidase PeiR-C90A
Authors: Guo, L.Z. / Wang, S.X. / Bai, L.p.
History
DepositionApr 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoisopeptidase PeiR
B: Endoisopeptidase PeiR
C: Endoisopeptidase PeiR
D: Endoisopeptidase PeiR


Theoretical massNumber of molelcules
Total (without water)104,9574
Polymers104,9574
Non-polymers00
Water10,016556
1
A: Endoisopeptidase PeiR
C: Endoisopeptidase PeiR


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-6 kcal/mol
Surface area19340 Å2
MethodPISA
2
B: Endoisopeptidase PeiR
D: Endoisopeptidase PeiR


Theoretical massNumber of molelcules
Total (without water)52,4782
Polymers52,4782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.476, 88.024, 87.412
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoisopeptidase PeiR


Mass: 26239.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter ruminantium M1 (archaea)
Gene: peiR, mru_0320 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DZZ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Salt:40.2 M Potassium phosphate dibasic; Precipitant:20% w/v Polyethylene glycol 3,350, pH 9.2;

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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: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.769→74.45 Å / Num. obs: 109917 / % possible obs: 92.39 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1211 / Rpim(I) all: 0.05176 / Rrim(I) all: 0.132 / Net I/σ(I): 8.72
Reflection shellResolution: 1.769→1.832 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.494 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 9277 / CC1/2: 0.677 / CC star: 0.899 / Rpim(I) all: 0.635 / Rrim(I) all: 1.627 / % possible all: 84.77

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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: 1.769→74.45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2601 5164 -
Rwork0.2271 --
obs-101628 92.39 %
Refinement stepCycle: LAST / Resolution: 1.769→74.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7366 0 0 557 7923
LS refinement shellResolution: 1.769→1.832 Å
RfactorNum. reflection
Rfree0.4937 482
Rwork0.4809 -
obs-9273

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