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- PDB-3nqy: Crystal structure of the autoprocessed complex of Vibriolysin MCP... -

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Basic information

Entry
Database: PDB / ID: 3nqy
TitleCrystal structure of the autoprocessed complex of Vibriolysin MCP-02 with a single point mutation E346A
Components(Secreted metalloprotease Mcp02) x 2
KeywordsHYDROLASE / autoprocessed complex / propeptide / thermolysin-like protease
Function / homology
Function and homology information


metalloendopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #490 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Nuclear Transport Factor 2; Chain: A, - #40 / Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal ...Nuclear Transport Factor 2; Chain: A, - #490 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Nuclear Transport Factor 2; Chain: A, - #40 / Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Secreted metalloprotease Mcp02
Similarity search - Component
Biological speciesPseudoalteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGao, X. / Wang, J. / Wu, J.-W. / Zhang, Y.-Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the autoprocessing of zinc metalloproteases in the thermolysin family
Authors: Gao, X. / Wang, J. / Yu, D.-Q. / Bian, F. / Xie, B.-B. / Chen, X.-L. / Zhou, B.-C. / Lai, L.-H. / Wang, Z.-X. / Wu, J.-W. / Zhang, Y.-Z.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Derived calculations
Revision 1.3Nov 1, 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 / 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_asym_id / _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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Secreted metalloprotease Mcp02
A: Secreted metalloprotease Mcp02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7964
Polymers53,6902
Non-polymers1052
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-58 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.009, 83.009, 154.216
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Secreted metalloprotease Mcp02 / MCP-02


Mass: 33912.812 Da / Num. of mol.: 1 / Fragment: the catalytic domain, residues 205-519 / Mutation: E346A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. (bacteria) / Strain: SM9913 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1DRD5, EC: 3.4.24.25
#2: Protein Secreted metalloprotease Mcp02 / MCP-02


Mass: 19777.289 Da / Num. of mol.: 1 / Fragment: propeptide domain, residues 25-204
Source method: isolated from a genetically manipulated source
Details: propeptide of MCP02 / Source: (gene. exp.) Pseudoalteromonas sp. (bacteria) / Strain: SM9913 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1DRD5, EC: 3.4.24.25
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTOPROCESSED COMPLEX

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 6000, 100mM Tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.48 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 2.6→23.7 Å / Num. all: 19363 / Num. obs: 19363 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 35.26 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 3 / Num. unique all: 19340 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NQX

3nqx


Resolution: 2.6→23.678 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8123 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 986 5.1 %
Rwork0.1959 18355 -
obs0.1988 19341 99.16 %
all-19341 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.968 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 89.25 Å2 / Biso mean: 33.6168 Å2 / Biso min: 17.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.2426 Å2-0 Å2-0 Å2
2--0.2426 Å20 Å2
3----0.4852 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 2 125 3796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083755
X-RAY DIFFRACTIONf_angle_d1.1955093
X-RAY DIFFRACTIONf_dihedral_angle_d18.141290
X-RAY DIFFRACTIONf_chiral_restr0.089546
X-RAY DIFFRACTIONf_plane_restr0.004674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6003-2.73720.31431350.22722603X-RAY DIFFRACTION100
2.7372-2.90850.31011400.22122569X-RAY DIFFRACTION100
2.9085-3.13260.2871670.2192572X-RAY DIFFRACTION100
3.1326-3.44690.26281420.18732627X-RAY DIFFRACTION100
3.4469-3.94370.24651210.16672640X-RAY DIFFRACTION99
3.9437-4.96120.17651500.15862615X-RAY DIFFRACTION99
4.9612-23.67950.24871310.2012729X-RAY DIFFRACTION97

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