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- PDB-3ami: The crystal structure of the M16B metallopeptidase subunit from S... -

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Basic information

Entry
Database: PDB / ID: 3ami
TitleThe crystal structure of the M16B metallopeptidase subunit from Sphingomonas sp. A1
Componentszinc peptidase
KeywordsHYDROLASE / alpha/beta / peptidase / zinc binding
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / : / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc peptidase active subunit
Similarity search - Component
Biological speciesSphingomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMaruyama, Y. / Chuma, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Heterosubunit composition and crystal structures of a novel bacterial M16B metallopeptidase
Authors: Maruyama, Y. / Chuma, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionAug 20, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: zinc peptidase
B: zinc peptidase


Theoretical massNumber of molelcules
Total (without water)98,9422
Polymers98,9422
Non-polymers00
Water3,999222
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-4 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.405, 139.757, 63.714
Angle α, β, γ (deg.)90.00, 107.91, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR DEFINED BIOLOGICAL UNIT: UNKNOWN. HOWEVER, AUTHOR CONFIRMED THE MOLECULAR TO BE MONOMER IN VITRO USING GEL FILTRATION COLUMN CHROMATOGRAPHY.

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Components

#1: Protein zinc peptidase


Mass: 49470.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: sp. A1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami (DE3)
References: UniProt: F2Z284*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO DDBJ, BUT IS NOT PUBLICLY AVAILABLE AT THE TIME ...THE SEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO DDBJ, BUT IS NOT PUBLICLY AVAILABLE AT THE TIME OF PROCESSING.

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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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% PEG 4000, 0.1M litium sulfate, 0.1M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32754 / % possible obs: 100 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 18.33
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→42.78 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.665 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26586 1659 5.1 %RANDOM
Rwork0.19622 ---
obs0.19982 31041 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20.65 Å2
2---1.08 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 0 222 6778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226707
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.9529106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9665848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75923.323313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.676151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.741565
X-RAY DIFFRACTIONr_chiral_restr0.0670.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215128
X-RAY DIFFRACTIONr_mcbond_it0.6481.54201
X-RAY DIFFRACTIONr_mcangle_it1.23926742
X-RAY DIFFRACTIONr_scbond_it1.82532506
X-RAY DIFFRACTIONr_scangle_it3.1764.52361
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 112 -
Rwork0.22 2242 -
obs--98.49 %

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