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- PDB-5hm9: Crystal structure of MamO protease domain from Magnetospirillum m... -

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Basic information

Entry
Database: PDB / ID: 5hm9
TitleCrystal structure of MamO protease domain from Magnetospirillum magneticum (apo form)
Components
  • MamO protease domain
  • poly(UNK)
KeywordsHYDROLASE / trypsin / biomineralization / pseudo-protease / magnetosome
Function / homology
Function and homology information


magnetosome membrane / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Transmembrane protein TauE-like / Sulfite exporter TauE/SafE / Peptidase S1C / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Probable membrane transporter protein MamO
Similarity search - Component
Biological speciesMagnetospirillum magneticum AMB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHershey, D.M. / Ren, X. / Hurley, J.H. / Komeili, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM084122 United States
Office of Naval ResearchN000141310421 United States
CitationJournal: Plos Biol. / Year: 2016
Title: MamO Is a Repurposed Serine Protease that Promotes Magnetite Biomineralization through Direct Transition Metal Binding in Magnetotactic Bacteria.
Authors: Hershey, D.M. / Ren, X. / Melnyk, R.A. / Browne, P.J. / Ozyamak, E. / Jones, S.R. / Chang, M.C. / Hurley, J.H. / Komeili, A.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MamO protease domain
C: poly(UNK)


Theoretical massNumber of molelcules
Total (without water)19,9382
Polymers19,9382
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-5 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.215, 130.215, 130.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432

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Components

#1: Protein MamO protease domain


Mass: 19494.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum AMB-1 (bacteria)
Gene: amb_0969 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: Q2W8Q2
#2: Protein/peptide poly(UNK)


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Unidentified peptide
Source: (gene. exp.) Magnetospirillum magneticum AMB-1 (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 50mM Na Acetate pH 4.6, 3.6M NH4Cl, 5% glycercol / PH range: 4.0 - 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12179 / % possible obs: 99.8 % / Redundancy: 15.2 % / Biso Wilson estimate: 56.38 Å2 / Rmerge(I) obs: 0.098 / Net I/av σ(I): 27.345 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.6412.30.695198.5
2.64-2.6912.80.677199.7
2.69-2.7413.10.59199.8
2.74-2.813.10.561199.8
2.8-2.8613.50.495199.8
2.86-2.9314.20.433199.8
2.93-314.40.3661100
3-3.0814.80.315199.8
3.08-3.1715.20.2531100
3.17-3.2815.80.211199.5
3.28-3.3916.20.171100
3.39-3.53160.15199.8
3.53-3.6915.90.1261100
3.69-3.8816.30.1111100
3.88-4.1316.70.0791100
4.13-4.4517.10.0671100
4.45-4.89170.068199.8
4.89-5.616.60.07199.8
5.6-7.0516.20.0611100
7.05-5015.60.042199.4

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Processing

Software
NameClassification
PHENIXrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KY9

1ky9


Resolution: 2.6→43.405 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.2322 602 4.94 %
Rwork0.2032 --
obs0.2047 12177 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.19 Å2 / Biso mean: 56.1871 Å2 / Biso min: 34.31 Å2
Refinement stepCycle: final / Resolution: 2.6→43.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 0 18 1416
Biso mean---47.12 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091425
X-RAY DIFFRACTIONf_angle_d1.1151948
X-RAY DIFFRACTIONf_chiral_restr0.051237
X-RAY DIFFRACTIONf_plane_restr0.006254
X-RAY DIFFRACTIONf_dihedral_angle_d14.643494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5991-2.86060.29961420.256228022944
2.8606-3.27440.32091590.241628202979
3.2744-4.12490.26311440.203528823026
4.1249-43.4110.17781570.18130713228

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