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- PDB-1gwa: Triiodide derivative of porcine pancreas elastase -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1gwa
TitleTriiodide derivative of porcine pancreas elastase
ComponentsELASTASE 1
KeywordsHYDROLASE / SERINE PROTEASE / ZYMOGEN
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.85 Å
AuthorsEvans, G. / Bricogne, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment
Authors: Evans, G. / Bricogne, G.
History
DepositionMar 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELASTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,98426
Polymers25,9291
Non-polymers3,05525
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.574, 57.899, 74.761
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 ELASTASE 1 /


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5
Details: PROTEIN SOLN: 5% PPE IN 0.1M CH3COONA PH5.0, 0.02% NAN3 RESERVOIR: 10MM CH3COONA, 10MM NASO4 DROP:5UL PROTEIN SOLN + 5UL RESERVOIR SITTING DROP VAPOUR DIFFUSION, pH 5.00
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 %PPE1drop
20.1 Msodium acetate1droppH5.0
30.02 %1dropNaN3
410 mMsodium acetate1reservoirpH5.0
510 mM1reservoirNa2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKUMSC / Detector: CCD / Date: Oct 15, 2001 / Details: OSMIC MIRRORS
RadiationMonochromator: MONOLAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→26.726 Å / Num. obs: 241027 / % possible obs: 99.2 % / Observed criterion σ(I): 6 / Redundancy: 12.5 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 6.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.344 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 26.68 Å
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameClassification
BUSTER-TNTrefinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.85→26.68 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.205 983 5 %RANDOM
Rwork0.169 ---
obs0.171 19184 99.2 %-
Refinement stepCycle: LAST / Resolution: 1.85→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 29 180 2031
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.663

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