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- PDB-1jiw: Crystal structure of the APR-APRin complex -

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Basic information

Entry
Database: PDB / ID: 1jiw
TitleCrystal structure of the APR-APRin complex
Components
  • ALKALINE METALLOPROTEINASE
  • PROTEINASE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Pseudomonas aeruginosa alkaline protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


symbiont-mediated evasion of recognition by host pattern recognition receptor / serralysin / negative regulation of complement activation, lectin pathway / negative regulation of complement activation, classical pathway / metalloendopeptidase inhibitor activity / positive regulation of sodium ion transport / metalloendopeptidase activity / peptidase activity / periplasmic space / calcium ion binding ...symbiont-mediated evasion of recognition by host pattern recognition receptor / serralysin / negative regulation of complement activation, lectin pathway / negative regulation of complement activation, classical pathway / metalloendopeptidase inhibitor activity / positive regulation of sodium ion transport / metalloendopeptidase activity / peptidase activity / periplasmic space / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Lipocalin - #10 / Metallo-peptidase family M12B Reprolysin-like / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal ...Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Lipocalin - #10 / Metallo-peptidase family M12B Reprolysin-like / 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, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Lipocalin / Neutral zinc metallopeptidases, zinc-binding region signature. / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serralysin / Proteinase inhibitor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHege, T. / Feltzer, R.E. / Gray, R.D. / Baumann, U.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of a complex between Pseudomonas aeruginosa alkaline protease and its cognate inhibitor: inhibition by a zinc-NH2 coordinative bond
Authors: Hege, T. / Feltzer, R.E. / Gray, R.D. / Baumann, U.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: ALKALINE METALLOPROTEINASE
I: PROTEINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,31411
Polymers60,9282
Non-polymers3869
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-100 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.627, 118.432, 91.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALKALINE METALLOPROTEINASE


Mass: 49531.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q03023, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein PROTEINASE INHIBITOR


Mass: 11396.819 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03026
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: tri-Na-citrate, isopropanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, temperature 291K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG40001reservoir
220 %isopropanol1reservoir
30.1 Mcitrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 11, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.74→14.93 Å / Num. all: 84588 / Num. obs: 84597 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.1 Å2 / Limit h max: 43 / Limit h min: 0 / Limit k max: 67 / Limit k min: 0 / Limit l max: 52 / Limit l min: 0 / Observed criterion F max: 2076195.96 / Observed criterion F min: 9.8
Reflection shellResolution: 1.74→1.77 Å / % possible all: 78.8
Reflection
*PLUS
Num. measured all: 310401 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 78.8 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKL

1akl


Resolution: 1.74→14.93 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6853 8.1 %random
Rwork0.184 ---
all0.185 85209 --
obs0.185 84497 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.9632 Å2 / ksol: 0.384305 e/Å3
Displacement parametersBiso max: 108.98 Å2 / Biso mean: 19.54 Å2 / Biso min: 1.13 Å2
Baniso -1Baniso -2Baniso -3
1--3.97 Å20 Å20 Å2
2--11.22 Å20 Å2
3----7.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Luzzati d res high-1.74
Refinement stepCycle: LAST / Resolution: 1.74→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 9 592 4898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg25.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.71
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.74-1.820.2168528.10.21791820.007105301003495.3
1.82-1.910.1998728.20.295750.007105841044798.7
1.91-2.030.1978598.10.19696430.007105591050299.5
2.03-2.190.1838377.90.18197260.006105841056399.8
2.19-2.410.1828357.90.18297390.006105891057499.8
2.41-2.760.1848858.30.18597800.006106711066599.9
2.76-3.470.1878517.90.18698560.006107151070799.9
3.47-14.930.178627.80.17101430.006110701100599.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8.1 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.216 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.217

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