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- PDB-7ecc: M4 family peptidase PlM4P-mature form -

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Basic information

Entry
Database: PDB / ID: 7ecc
TitleM4 family peptidase PlM4P-mature form
ComponentsM4 family peptidase
KeywordsHYDROLASE / peptidase
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesPseudoalteromonas lipolytica SCSIO 04301 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, J.
CitationJournal: To Be Published
Title: M4 family peptidase PlM4P-mature form
Authors: Yang, J.
History
DepositionMar 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M4 family peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1104
Polymers34,9101
Non-polymers2003
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-49 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.738, 85.272, 85.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein M4 family peptidase


Mass: 34909.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas lipolytica SCSIO 04301 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Molecular Dimensions Morpheus II C12: 4mM Alkalis, 0.1M buffer 6, 31% precipitant mix 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2→20.13 Å / Num. obs: 22253 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.085 / Rrim(I) all: 0.262 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.055.71.609901215890.6420.7351.7740.599.9
8.94-20.1211.20.11330442720.990.0340.11811.391.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nqx

3nqx


Resolution: 2→20.13 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.583 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 1111 5.3 %RANDOM
Rwork0.2376 ---
obs0.2401 19952 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.96 Å2 / Biso mean: 21.632 Å2 / Biso min: 9.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å2-0 Å20 Å2
2--3.22 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 2→20.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 7 159 2441
Biso mean--28.01 28.43 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132339
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181922
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6323184
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5714479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29925.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70315328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.816153
X-RAY DIFFRACTIONr_chiral_restr0.0720.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 97 -
Rwork0.331 1456 -
all-1553 -
obs--97.86 %

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