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- PDB-1hyl: THE 1.8 A STRUCTURE OF COLLAGENASE FROM HYPODERMA LINEATUM -

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Basic information

Entry
Database: PDB / ID: 1hyl
TitleTHE 1.8 A STRUCTURE OF COLLAGENASE FROM HYPODERMA LINEATUM
ComponentsHYPODERMA LINEATUM COLLAGENASE
KeywordsHYDROLASE (SERINE PROTEASE)
Function / homology
Function and homology information


hypodermin C / collagen catabolic process / serine-type endopeptidase activity / proteolysis / extracellular region
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
Biological speciesHypoderma lineatum (early cattle grub)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBroutin, I. / Arnoux, B. / Riche, C. / Lecroisey, A. / Keil, B. / Pascard, C. / Ducruix, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: 1.8 A structure of Hypoderma lineatum collagenase: a member of the serine proteinase family.
Authors: Broutin, I. / Arnoux, B. / Riche, C. / Lecroisey, A. / Keil, B. / Pascard, C. / Ducruix, A.
History
DepositionMay 2, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPODERMA LINEATUM COLLAGENASE
B: HYPODERMA LINEATUM COLLAGENASE


Theoretical massNumber of molelcules
Total (without water)50,4942
Polymers50,4942
Non-polymers00
Water5,314295
1
A: HYPODERMA LINEATUM COLLAGENASE
B: HYPODERMA LINEATUM COLLAGENASE

A: HYPODERMA LINEATUM COLLAGENASE
B: HYPODERMA LINEATUM COLLAGENASE


Theoretical massNumber of molelcules
Total (without water)100,9894
Polymers100,9894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)111.700, 111.700, 165.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein HYPODERMA LINEATUM COLLAGENASE


Mass: 25247.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypoderma lineatum (early cattle grub)
References: UniProt: P08897, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlHLC11
250 mMTris11
360 mM11NaCl
41.23 Mammonium sulfate11

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Data collection

DetectorDate: Dec 4, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→15.4 Å / Num. obs: 42152 / % possible obs: 74 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 51 %

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Processing

Software
NameVersionClassification
MADNESdata collection
X-PLOR2.1model building
X-PLOR2.1refinement
MADNESdata reduction
X-PLOR2.1phasing
RefinementResolution: 1.8→8 Å
RfactorNum. reflection% reflection
Rwork0.183 --
obs0.183 38849 80.7 %
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 295 3851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 39231
Solvent computation
*PLUS
Displacement parameters
*PLUS

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