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- PDB-3nqx: Crystal structure of vibriolysin MCP-02 mature enzyme, a zinc met... -

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Basic information

Entry
Database: PDB / ID: 3nqx
TitleCrystal structure of vibriolysin MCP-02 mature enzyme, a zinc metalloprotease from M4 family
ComponentsSecreted metalloprotease Mcp02
KeywordsHYDROLASE / Zinc metalloprotease / alpha/beta protein
Function / homology
Function and homology information


metalloendopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain ...Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / 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 / 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: 1.7 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 1.2Dec 2, 2014Group: Structure summary
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_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted metalloprotease Mcp02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1533
Polymers33,0481
Non-polymers1052
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.801, 73.792, 91.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Secreted metalloprotease Mcp02 / MCP-02


Mass: 33047.922 Da / Num. of mol.: 1 / Fragment: the catalytic domain, residues 205-510
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 3000, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.48 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.7→21.45 Å / Num. all: 32935 / Num. obs: 32935 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 54
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 9 / Num. unique all: 32935 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EZM

1ezm


Resolution: 1.7→21.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.896 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21739 1669 5.1 %RANDOM
Rwork0.17433 ---
obs0.17649 31266 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.182 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 2 437 2716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9133181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13125.328122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27415328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.336156
X-RAY DIFFRACTIONr_chiral_restr0.1710.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021888
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.21344
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21635
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2324
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.51497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36122321
X-RAY DIFFRACTIONr_scbond_it2.5323989
X-RAY DIFFRACTIONr_scangle_it3.4124.5860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 110 -
Rwork0.272 2063 -
obs--89.5 %

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