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

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Basic information

Entry
Database: PDB / ID: 5hma
TitleCrystal structure of MamO protease domain from Magnetospirillum magneticum (Ni bound form)
Components
  • Trypsin-like serine protease
  • Unidentified peptide
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
NICKEL (II) ION / Probable membrane transporter protein MamO
Similarity search - Component
Biological speciesMagnetospirillum magneticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 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 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-like serine protease
C: Unidentified peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2304
Polymers20,1362
Non-polymers942
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-24 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.163, 129.163, 129.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-451-

HOH

31A-454-

HOH

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Components

#1: Protein Trypsin-like serine protease


Mass: 19692.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (bacteria)
Strain: AMB-1 / ATCC 700264 / Gene: amb0969 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: Q2W8Q2
#2: Protein/peptide Unidentified peptide


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (bacteria)
Strain: AMB-1 / ATCC 700264 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.47 Å3/Da / Density % sol: 72.51 % / Description: Cubic
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 50mM Na Acetate pH 4.6, 3.6M NH4Cl, 5% glycerol / 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: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 16999 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 51.17 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 1.078 / Net I/av σ(I): 29.755 / Net I/σ(I): 12.3 / Num. measured all: 214349
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3413.10.8978480.8580.2560.9331.149100
2.34-2.3813.10.6878150.9050.1960.7151.161100
2.38-2.4313.10.6318350.9290.180.6571.125100
2.43-2.48130.5628290.9450.1610.5851.147100
2.48-2.5313.20.4728250.9580.1340.4911.139100
2.53-2.59130.3958210.9660.1130.4111.108100
2.59-2.6613.10.3248430.9770.0930.3381.095100
2.66-2.73130.278310.9820.0770.2811.06100
2.73-2.81130.2388330.9850.0680.2481.08199.9
2.81-2.9130.1928310.990.0550.21.06499.9
2.9-312.90.1568390.9930.0450.1621.068100
3-3.1212.90.1388360.9940.040.1441.07399.9
3.12-3.2612.80.1088500.9940.0310.1131.088100
3.26-3.4412.80.0948420.9970.0270.0981.02399.9
3.44-3.6512.70.0838540.9970.0240.0861.019100
3.65-3.9312.30.0748560.9970.0220.0781.06599.9
3.93-4.3311.70.0698590.9970.0210.0721.05699.7
4.33-4.9511.10.0668780.9970.0210.0690.99999.8
4.95-6.2411.60.0588940.9970.0180.0610.93299.8
6.24-5011.20.0379800.9990.0110.0391.08599.3

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Processing

Software
NameClassification
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MH9

5mh9
PDB Unreleased entry


Resolution: 2.299→45.666 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 831 4.89 %
Rwork0.1839 16162 -
obs0.1852 16993 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.86 Å2 / Biso mean: 63.2227 Å2 / Biso min: 35.1 Å2
Refinement stepCycle: final / Resolution: 2.299→45.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 2 55 1469
Biso mean--88.71 58.19 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081444
X-RAY DIFFRACTIONf_angle_d1.091978
X-RAY DIFFRACTIONf_chiral_restr0.053241
X-RAY DIFFRACTIONf_plane_restr0.005256
X-RAY DIFFRACTIONf_dihedral_angle_d13.89498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2992-2.44320.31551450.236626182763100
2.4432-2.63180.25421340.228226362770100
2.6318-2.89660.2581350.207726412776100
2.8966-3.31570.21951420.20126592801100
3.3157-4.1770.20821250.177127252850100
4.177-45.6750.1761500.16422883303399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.81390.8068-1.05473.6051-1.41083.8513-0.03280.0227-0.2518-0.0997-0.07880.0120.21270.11550.12090.35840.0112-0.01630.25470.01050.3983534.8727206.8948119.1554
24.02570.57910.04124.9656-0.72685.059-0.13930.23840.24810.0725-0.0004-0.3412-0.05310.58120.11290.3788-0.0297-0.02570.38740.04150.3972543.5296218.6279113.3577
33.4782-1.66180.29866.77331.49853.40352.1292-1.33981.9581.4709-0.9083-0.35650.55-0.3824-1.18180.6158-0.29720.0270.61170.07211.2474550.3685218.6377125.1966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 121 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 224 )A0
3X-RAY DIFFRACTION3chain 'C' and (resid 103 through 107 )C0

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