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- PDB-3hbu: PrtC methionine mutants: M226H DESY -

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Basic information

Entry
Database: PDB / ID: 3hbu
TitlePrtC methionine mutants: M226H DESY
Components
  • Secreted protease C
  • 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 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 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 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description ...Data collection / Refinement description / Source and taxonomy / Structure summary
Category: diffrn_source / pdbx_entity_src_syn ...diffrn_source / pdbx_entity_src_syn / software / struct_keywords
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 / _struct_keywords.text
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_alt_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_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.pdbx_ptnr1_label_alt_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_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: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,68114
Polymers50,1342
Non-polymers54812
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-92 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.112, 102.112, 122.863
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-816-

HOH

21P-906-

HOH

31P-911-

HOH

41P-929-

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: 49773.113 Da / Num. of mol.: 1 / Mutation: M226H
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 peptide /


Mass: 360.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 498 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.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 486 / 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: 3.68 Å3/Da / Density % sol: 66.59 %
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
DetectorType: MAR165 / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 72602 / Num. obs: 72602 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.04 / Χ2: 0.937 / Net I/σ(I): 53.772
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 10.2 / Num. unique all: 3598 / Χ2: 0.569 / % 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
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GO8

1go8


Resolution: 1.77→37.162 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.901 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2138 2.95 %random
Rwork0.166 ---
all0.167 ---
obs0.167 72451 99.85 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.737 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 324.66 Å2 / Biso mean: 34.766 Å2 / Biso min: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.592 Å20 Å2-0 Å2
2--1.592 Å2-0 Å2
3----3.185 Å2
Refinement stepCycle: LAST / Resolution: 1.77→37.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 12 486 4047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093636
X-RAY DIFFRACTIONf_angle_d1.6284939
X-RAY DIFFRACTIONf_chiral_restr0.084512
X-RAY DIFFRACTIONf_plane_restr0.005666
X-RAY DIFFRACTIONf_dihedral_angle_d18.0381204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.77-1.8110.2111400.16546574797
1.811-1.8570.1971210.15846694790
1.857-1.9070.1881470.15646094756
1.907-1.9630.1791280.14846684796
1.963-2.0260.191410.14946224763
2.026-2.0990.1991440.14446564800
2.099-2.1830.1681320.14646844816
2.183-2.2820.151480.14846684816
2.282-2.4020.1751240.15346544778
2.402-2.5530.1871480.15946924840
2.553-2.750.1951440.16646784822
2.75-3.0260.2021490.16646704819
3.026-3.4640.1681650.15746844849
3.464-4.3630.1541390.14647824921
4.363-37.1710.2041680.18849205088
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)
11.09310.1996-0.50410.2201-0.18360.52340.09270.0450.18820.0027-0.00570.0732-0.0842-0.0826-0.10350.0380.02180.03540.069-0.00780.074939.242550.394342.1367
20.05930.1848-0.30740.4575-0.38021.3098-0.00110.06540.05430.01370.04920.1642-0.0275-0.237-0.0446-0.0259-0.00460.00710.0936-0.00110.071450.423252.051621.9863
30.5602-0.22540.18950.6584-0.41630.2687-0.07950.25070.0648-0.10130.0698-0.0128-0.0408-0.07070.00460.1024-0.0209-0.03610.14440.05630.074961.978764.9922-1.9793
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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