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- PDB-2pwa: Crystal Structure of the complex of Proteinase K with Alanine Bor... -

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Basic information

Entry
Database: PDB / ID: 2pwa
TitleCrystal Structure of the complex of Proteinase K with Alanine Boronic acid at 0.83A resolution
ComponentsProteinase K
KeywordsHYDROLASE / PROTEINASE K / Alanine boronic acid
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE BORONIC ACID / NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.83 Å
AuthorsJain, R. / Singh, N. / Perbandt, M. / Betzel, C. / Sharma, S. / Kaur, P. / Srinivasan, A. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of Proteinase K with Alanine Boronic Acid at 0.83A Resolution
Authors: Jain, R. / Singh, N. / Perbandt, M. / Betzel, C. / Sharma, S. / Kaur, P. / Srinivasan, A. / Singh, T.P.
History
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE Amino acid 207 was mutated by persuing electron density at atomic resolution and after ...SEQUENCE Amino acid 207 was mutated by persuing electron density at atomic resolution and after repeation of many refinement cycle.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,83114
Polymers28,9591
Non-polymers87213
Water9,638535
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.302, 67.302, 106.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Proteinase K / / Tritirachium alkaline proteinase / Endopeptidase K


Mass: 28958.791 Da / Num. of mol.: 1 / Fragment: Proteinase K / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K

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Non-polymers , 5 types, 548 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-B2A / ALANINE BORONIC ACID


Type: peptide-like / Mass: 88.901 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8BNO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CaCl2 & NaNO3,alanine boronic acid, pH 6.5, VAPOR DIFFUSION, temperature 295K, pH 6.50, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2006 / Details: mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 0.83→56.89 Å / Num. all: 220399 / Num. obs: 220399 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.2 % / Biso Wilson estimate: 6.08 Å2 / Rsym value: 0.043 / Net I/σ(I): 40.7
Reflection shellResolution: 0.83→0.84 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.0544 / % possible all: 92.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 0.83→10 Å / Num. parameters: 24726 / Num. restraintsaints: 29442 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1363 2215 1 %RANDOM
Rwork0.1202 ---
obs0.1202 218184 95.4 %-
all-220399 --
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 1957 / Occupancy sum non hydrogen: 2651.4
Refinement stepCycle: LAST / Resolution: 0.83→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 54 535 2707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.055
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0321
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.108
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.13
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.109
LS refinement shellHighest resolution: 0.83 Å
RfactorNum. reflection% reflection
Rfree0.12 2215 -
Rwork0.108 --
obs-218184 95.7 %

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