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- PDB-4k89: Crystal structure of Pseudomonas aeruginosa strain K solvent tole... -

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Basic information

Entry
Database: PDB / ID: 4k89
TitleCrystal structure of Pseudomonas aeruginosa strain K solvent tolerant elastase
ComponentsOrganic solvent tolerant elastase
KeywordsHYDROLASE / Calcium binding / Zinc binding / Phosphate Binding
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / extracellular region / metal ion binding
Similarity search - Function
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 ...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
PHOSPHATE ION / Neutral metalloproteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsAli, M.S.M. / Said, Z.S.A.M. / Rahman, R.N.Z.R.A. / Basri, M. / Salleh, A.B.
CitationJournal: To be Published
Title: Crystal structure analysia of solvent tolerant elastase strain K
Authors: Ali, M.S.M. / Said, Z.S.A.M. / Rahman, R.N.Z.R.A. / Basri, M. / Salleh, A.B.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Organic solvent tolerant elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,90410
Polymers33,1461
Non-polymers7599
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.99, 90.173, 40.60
Angle α, β, γ (deg.)90.00, 113.814, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Organic solvent tolerant elastase


Mass: 33145.504 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 198-498 / Mutation: G313D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K / Gene: HindIII1500PstI / Plasmid: pCON2(3) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: A7LI11

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Non-polymers , 5 types, 195 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 298 K / Method: seeding-capillary counter diffusion / pH: 8.7
Details: 0.1M sodium citrate tribasic dihydrate pH5.6, 1.0M Ammonium phosphate monobasic, pH 8.7, seeding-capillary counter diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 21, 2012
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. all: 385687 / Num. obs: 385687 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 33.358
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
autoMRmodel building
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
autoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→45.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.941 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19136 2603 5.1 %RANDOM
Rwork0.16711 ---
obs0.16836 51267 99.78 %-
all-51334 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.39→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 41 186 2542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0212411
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6431.9323263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11223.525122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98715347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7041515
X-RAY DIFFRACTIONr_chiral_restr0.160.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211905
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_it1.5951.51465
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49622329
X-RAY DIFFRACTIONr_scbond_it3.43946
X-RAY DIFFRACTIONr_scangle_it5.174.5934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.391→1.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 187 -
Rwork0.232 3541 -
obs--98.68 %

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