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- PDB-8z4h: Pseudomurein Endoisopeptidase PeiR -

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Basic information

Entry
Database: PDB / ID: 8z4h
TitlePseudomurein Endoisopeptidase PeiR
ComponentsEndoisopeptidase PeiR
KeywordsHYDROLASE / Methanogenic archaea / pseudomurein / endopeptidases
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: 1.79 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
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)105,0854
Polymers105,0854
Non-polymers00
Water8,161453
1
A: Endoisopeptidase PeiR
C: Endoisopeptidase PeiR


Theoretical massNumber of molelcules
Total (without water)52,5432
Polymers52,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-6 kcal/mol
Surface area19480 Å2
MethodPISA
2
B: Endoisopeptidase PeiR
D: Endoisopeptidase PeiR


Theoretical massNumber of molelcules
Total (without water)52,5432
Polymers52,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-5 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.828, 86.916, 87.993
Angle α, β, γ (deg.)90.00, 91.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoisopeptidase PeiR


Mass: 26271.289 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.: 453 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Precipitant:25% w/v Polyethylene glycol 3,350; Buffer:0.1 M HEPES pH 7.5; Salt :0.2 M Ammonium sulfate;

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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: 1.79→73.79 Å / Num. obs: 95039 / % possible obs: 90.86 % / Redundancy: 2.77 % / CC1/2: 0.994 / Rmerge(I) obs: 0.0676 / Net I/σ(I): 5.05
Reflection shellResolution: 1.79→1.86 Å / Rmerge(I) obs: 0.7698 / Num. unique obs: 4647

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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: 1.79→73.79 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 39.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2852 4674 4.93 %
Rwork0.2531 --
obs0.2546 94808 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→73.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 0 453 7824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0317557
X-RAY DIFFRACTIONf_angle_d3.85810194
X-RAY DIFFRACTIONf_dihedral_angle_d12.1141030
X-RAY DIFFRACTIONf_chiral_restr0.2541044
X-RAY DIFFRACTIONf_plane_restr0.0331299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.55421350.52442398X-RAY DIFFRACTION74
1.81-1.830.50921290.50772625X-RAY DIFFRACTION79
1.83-1.860.49911370.47422885X-RAY DIFFRACTION87
1.86-1.880.46641320.46412855X-RAY DIFFRACTION87
1.88-1.90.4641940.4532042X-RAY DIFFRACTION61
1.9-1.930.4576840.44342381X-RAY DIFFRACTION71
1.93-1.960.50211180.442215X-RAY DIFFRACTION68
1.96-1.990.40921750.36873272X-RAY DIFFRACTION100
1.99-2.020.39331700.35293287X-RAY DIFFRACTION100
2.02-2.050.37181780.35583300X-RAY DIFFRACTION100
2.05-2.090.42251220.36032426X-RAY DIFFRACTION75
2.09-2.120.3331790.32363285X-RAY DIFFRACTION100
2.12-2.170.35951970.30863300X-RAY DIFFRACTION100
2.17-2.210.33091940.28943251X-RAY DIFFRACTION100
2.21-2.260.30511480.28222583X-RAY DIFFRACTION79
2.26-2.310.29471900.26563257X-RAY DIFFRACTION99
2.31-2.370.31071980.27763242X-RAY DIFFRACTION100
2.37-2.430.32131700.26253319X-RAY DIFFRACTION100
2.43-2.50.3211700.24793281X-RAY DIFFRACTION100
2.5-2.580.28941510.24613328X-RAY DIFFRACTION100
2.58-2.660.28271540.24712745X-RAY DIFFRACTION99
2.68-2.780.30132000.25223208X-RAY DIFFRACTION98
2.78-2.910.29731760.25323324X-RAY DIFFRACTION100
2.91-3.060.2771330.23483339X-RAY DIFFRACTION100
3.06-3.260.30121540.2323333X-RAY DIFFRACTION100
3.26-3.510.23091300.22542941X-RAY DIFFRACTION88
3.51-3.860.26141390.20752999X-RAY DIFFRACTION90
3.86-4.420.19311390.17683041X-RAY DIFFRACTION90
4.42-5.570.2111980.17753321X-RAY DIFFRACTION100
5.57-100.21191800.21193351X-RAY DIFFRACTION99

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