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- PDB-3hbv: PrtC methionine mutants: M226A in-house -

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Basic information

Entry
Database: PDB / ID: 3hbv
TitlePrtC methionine mutants: M226A in-house
Components
  • Secreted protease C
  • Uncharacterized peptide
KeywordsHYDROLASE / Met-turn / beta roll / zinc / metalloprotease / metzincin / Calcium / Metal-binding / Protease / Secreted / Zymogen
Function / homology
Function and homology information


serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat ...Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesErwinia chrysanthemi (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U.
CitationJournal: Biol.Chem. / Year: 2009
Title: Metzincin's canonical methionine is responsible for the structural integrity of the zinc-binding site
Authors: Oberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U.
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 27, 2021Group: Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Secreted protease C
Z: Uncharacterized peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90615
Polymers50,3532
Non-polymers55313
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-152 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.961, 101.961, 123.222
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11P-538-

HOH

21P-853-

HOH

31P-953-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules PZ

#1: Protein Secreted protease C / ProC


Mass: 49706.043 Da / Num. of mol.: 1 / Mutation: M226A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Gene: prtC / Plasmid: pUC18 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE
References: UniProt: P16317, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide Uncharacterized peptide


Mass: 646.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 4 types, 585 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHOR STATES THAT THE ORIGIN OF THE PEPTIDE IS UNCLEAR. THE SEQUENCE IS BASED ON THE SHAPE OF ...THE AUTHOR STATES THAT THE ORIGIN OF THE PEPTIDE IS UNCLEAR. THE SEQUENCE IS BASED ON THE SHAPE OF THE ELECTRON DENSITY MAP.

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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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M NaCl, 0.1 M phosphate, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Type: RIGAKU RU300 / Wavelength: 0.812 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2003 / Details: Si[111], mirrors
RadiationMonochromator: RIGAKU OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 54277 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 3.773
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.5 / Num. unique all: 2670 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.4_54refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GO8

1go8


Resolution: 1.95→29.346 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.915 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML / Details: 14.55
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1629 3.01 %random
Rwork0.153 ---
obs0.153 54147 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.843 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 87.58 Å2 / Biso mean: 27.888 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.337 Å2-0 Å2-0 Å2
2--1.337 Å2-0 Å2
3----2.673 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 13 572 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072992
X-RAY DIFFRACTIONf_angle_d1.0084061
X-RAY DIFFRACTIONf_chiral_restr0.074428
X-RAY DIFFRACTIONf_plane_restr0.004545
X-RAY DIFFRACTIONf_dihedral_angle_d17.947993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0080.1581420.14443384480100
2.008-2.0720.1621190.13343554474100
2.072-2.1470.1711290.1343254454100
2.147-2.2330.1381500.13543254475100
2.233-2.3340.1591200.14443594479100
2.334-2.4570.2081060.15143994505100
2.457-2.6110.2051520.15743364488100
2.611-2.8120.1721360.15543834519100
2.812-3.0950.1741410.15643894530100
3.095-3.5420.1521430.13843814524100
3.542-4.460.1311310.1344433456499
4.46-29.3490.1721600.174495465598
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)
10.6650.399-0.48320.3394-0.27390.33940.0614-0.0610.01860.0309-0.03660.0051-0.03770.0704-0.00990.07590.00110.02260.1399-0.01630.082240.493544.030549.1141
20.07910.0924-0.25880.126-0.13230.57190.00030.05010.0421-0.00060.01290.09470.0098-0.1561-0.00870.0647-0.00780.00420.1535-0.00740.121351.821651.890721.5409
30.44050.0237-0.00390.5409-0.32310.2075-0.04060.2570.085-0.11960.09120.02530.0084-0.095-0.04410.1265-0.01-0.02390.18370.06390.130761.796664.8609-1.9626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 10:225 and chain PP10 - 225
2X-RAY DIFFRACTION2resid 226:400 and chain PP226 - 400
3X-RAY DIFFRACTION3resid 401:495 and chain PP401 - 495

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