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- PDB-3vi1: Crystal structure of Pseudomonas aerginosa alkaline protease comp... -

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Basic information

Entry
Database: PDB / ID: 3vi1
TitleCrystal structure of Pseudomonas aerginosa alkaline protease complexed with Substance P(1-6)
Components
  • Alkaline metalloproteinase
  • Substance P1-6, RPKPQQ
KeywordsHYDROLASE / Calcium Binding / Zinc Binding
Function / homology
Function and homology information


serralysin / negative regulation of complement activation, lectin pathway / negative regulation of complement activation, classical pathway / positive regulation of sodium ion transport / metalloendopeptidase activity / peptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Metallo-peptidase family M12B Reprolysin-like / 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. ...Metallo-peptidase family M12B Reprolysin-like / 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, 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMatoba, K. / Harada, S.
CitationJournal: To be Published
Title: Crystal structure of Pseudomonas aerginosa alkaline protease complexed with Substance P(1-6)
Authors: Matoba, K. / Harada, S.
History
DepositionSep 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_asym_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_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
A: Alkaline metalloproteinase
B: Alkaline metalloproteinase
C: Substance P1-6, RPKPQQ
D: Substance P1-6, RPKPQQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,34522
Polymers100,5734
Non-polymers77218
Water4,738263
1
A: Alkaline metalloproteinase
C: Substance P1-6, RPKPQQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,67211
Polymers50,2862
Non-polymers3869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-6 kcal/mol
Surface area18270 Å2
MethodPISA
2
B: Alkaline metalloproteinase
D: Substance P1-6, RPKPQQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,67211
Polymers50,2862
Non-polymers3869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-5 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.400, 79.720, 149.000
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 Alkaline metalloproteinase / AP


Mass: 49531.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1
References: UniProt: Q03023, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide Substance P1-6, RPKPQQ


Mass: 754.876 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide were synthesized by conventional solid phase techniques using Fmoc (N-(9-fluorenyl)methoxycarbonyl) chemistry by an automatic peptide synsethesizer
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 33% PEG20000, 0.1M acetate buffer, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 21, 2007
RadiationMonochromator: Confocal ellipical mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.51 Å / Num. obs: 63706 / % possible obs: 98.2 % / Redundancy: 2.36 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2-2.072.250.3692.46359198.3
2.07-2.152.340.3352.564361100
2.15-2.252.350.3052.864171100
2.25-2.372.360.2683.16385199.8
2.37-2.522.360.2263.56414199.7
2.52-2.712.360.1933.96407199.4
2.71-2.992.370.1524.96418198.9
2.99-3.422.380.1027.26420198.5
3.42-4.312.370.05712.96349196.8
4.31-37.32.480.03520.36201190.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKL

1akl


Resolution: 2→38.51 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.749 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22485 2885 5.1 %RANDOM
Rwork0.21146 ---
obs0.21214 53607 88.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 0 18 263 7364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0217297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8431.9319925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7815950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82425.63357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1371519
X-RAY DIFFRACTIONr_chiral_restr0.0550.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215791
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1191.54688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.22127409
X-RAY DIFFRACTIONr_scbond_it0.24232609
X-RAY DIFFRACTIONr_scangle_it0.4084.52515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 218 -
Rwork0.265 3795 -
obs--86.75 %
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)
10.6009-1.3581-0.43643.10310.97460.3533-0.1161-0.0202-0.1170.19270.0860.27870.0625-0.03560.03010.0898-0.02450.0180.14110.02340.1336-4.733114.139425.0971
20.53870.2488-0.03370.9054-0.09340.2878-0.03620.00490.0691-0.12360.03490.0872-0.029-0.04520.00130.05650.0072-0.00020.0853-0.00580.0836-4.026450.18520.073
30.30420.14180.11290.59150.00550.0626-0.0047-0.06990.03310.02220.0191-0.0155-0.0049-0.004-0.01440.07480.0051-0.0050.0973-0.01640.11073.120646.840625.9796
40.00880.0239-0.02710.83090.04620.131-0.0154-0.00760.0002-0.02160.01070.00410.00860.02760.00480.07920.00620.00610.1011-0.0060.09827.75518.689614.192
50.61140.9820.87053.16621.00571.33870.0437-0.0674-0.00060.026-0.05690.0060.069-0.11610.01320.0567-0.00310.02470.0772-0.00590.10540.8761-7.12197.2523
60.2139-0.28190.11021.1922-0.12930.3077-0.0059-0.01240.01530.115-0.02780.06380.0244-0.10260.03370.0527-0.00960.01310.0966-0.02860.0776-4.004-9.7564-20.4868
70.6150.92811.06592.15181.18972.10950.0759-0.0117-0.0106-0.0271-0.0451-0.03740.1659-0.0228-0.03080.10550.0514-0.01430.0853-0.01890.09878.531-31.0902-28.2239
80.2724-0.1279-0.08311.10170.12060.36640.02280.0652-0.05920.0022-0.0118-0.00160.0333-0.0048-0.0110.08560.00490.00180.0765-0.00940.09915.5846-23.3946-24.5508
90.4750.28570.05240.41580.09520.2699-0.02090.04610.00360.0188-0.01330.03740.01390.03640.03420.07750.0030.00410.0901-0.00440.10124.8943-3.4476-21.5984
100.2879-0.3888-0.16571.17640.44550.36280.0089-0.02050.0029-0.0313-0.02970.0455-0.0145-0.00440.02090.0692-0.0067-0.02050.0895-0.01060.10192.834425.5137-10.9162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 24
2X-RAY DIFFRACTION2A25 - 74
3X-RAY DIFFRACTION3A75 - 240
4X-RAY DIFFRACTION4A241 - 409
5X-RAY DIFFRACTION5A410 - 470
6X-RAY DIFFRACTION6B1 - 68
7X-RAY DIFFRACTION7B69 - 100
8X-RAY DIFFRACTION8B101 - 194
9X-RAY DIFFRACTION9B195 - 325
10X-RAY DIFFRACTION10B326 - 470

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