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- PDB-3hda: PrtC methionine mutants: M226A_DESY -

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Basic information

Entry
Database: PDB / ID: 3hda
TitlePrtC methionine mutants: M226A_DESY
Components
  • Secreted protease C
  • Uncharacterized peptide
KeywordsHYDROLASE / Met-turn / beta roll / metalloprotease / metzincin / 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 M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / 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 M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.131 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 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 17, 2016Group: Refinement description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / pdbx_entity_src_syn / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 1.6Sep 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)50,61711
Polymers50,2662
Non-polymers3519
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-63 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.858, 101.858, 122.521
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-648-

HOH

21P-650-

HOH

31P-680-

HOH

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Components

#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: 559.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
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: 3.65 Å3/Da / Density % sol: 66.26 %
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2003 / Details: Mirrors
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. all: 41603 / Num. obs: 41603 / % possible obs: 99.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Χ2: 0.968 / Net I/σ(I): 19.709
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.396 / Num. unique all: 2043 / Χ2: 0.959 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1go8


Resolution: 2.131→26.508 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1260 3.04 %random
Rwork0.182 ---
obs0.183 41498 99.83 %-
all-41498 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.016 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 105.85 Å2 / Biso mean: 35.693 Å2 / Biso min: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.234 Å2-0 Å2-0 Å2
2--1.234 Å2-0 Å2
3----2.468 Å2
Refinement stepCycle: LAST / Resolution: 2.131→26.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 9 227 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053008
X-RAY DIFFRACTIONf_angle_d0.8824086
X-RAY DIFFRACTIONf_chiral_restr0.059429
X-RAY DIFFRACTIONf_plane_restr0.003550
X-RAY DIFFRACTIONf_dihedral_angle_d17.345999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.131-2.2160.2481500.21944184568100
2.216-2.3170.2591180.22744144532100
2.317-2.4390.2261130.19144554568100
2.439-2.5910.2561460.18944294575100
2.591-2.7910.2181420.1944424584100
2.791-3.0720.2361370.1884430456799
3.072-3.5150.1941560.1744714627100
3.515-4.4260.1781350.15345284663100
4.426-26.510.1671630.17246514814100
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)
10.8050.6451-0.50610.8143-0.29680.95080.0852-0.10740.03840.0371-0.04840.0077-0.06830.05-0.02490.2010.01380.03910.2932-0.01970.214540.143344.016448.6984
20.30870.2487-0.60270.274-0.36051.5004-0.01040.05330.07160.01370.02670.11670.0346-0.2348-0.01720.1732-0.00370.00630.2982-0.00190.245351.583752.012721.2727
31.221-0.01950.30620.9403-0.88530.9198-0.08550.40990.1921-0.14690.05830.0308-0.0417-0.12370.01670.2537-0.0153-0.02510.33070.07960.234761.475164.7613-1.6641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 10:225P - S0
2X-RAY DIFFRACTION2resid 226:400P - S0
3X-RAY DIFFRACTION3resid 401:495P - S0

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