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- PDB-2hlc: HL COLLAGENASE STRUCTURE AT 1.7A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2hlc
TitleHL COLLAGENASE STRUCTURE AT 1.7A RESOLUTION
ComponentsCOLLAGENASE
KeywordsSERINE PROTEASE / HYDROLASE / COLLAGEN DEGRADATION
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 / SYNCHROTRON / RIGID BODY / Resolution: 1.7 Å
AuthorsBroutin, I. / Merigeau, K. / Arnoux, B. / Ducruix, A.
Citation
Journal: 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.
#1: Journal: To be Published
Title: Collagenase-Collagenase Interactions, a Descriptor for the Mapping of the Binding Site
Authors: Broutin, I. / Merigeau, K. / Arnoux, B. / Ducruix, A.
#2: Journal: To be Published
Title: Crystallographic Analyses of Lysozyme and Collagenase Space Grown Crystals Versus Ground Controls
Authors: Broutin, I. / Ries-Kautt, M. / Ducruix, A.
History
DepositionJan 8, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGENASE
B: COLLAGENASE


Theoretical massNumber of molelcules
Total (without water)50,4942
Polymers50,4942
Non-polymers00
Water6,179343
1
A: COLLAGENASE
B: COLLAGENASE

A: COLLAGENASE
B: 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)111.300, 111.300, 165.680
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 COLLAGENASE /


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


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.54 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion - hanging drop in microgravity / pH: 7
Details: PROTEIN CONCENTRATION WAS 10MG/ML. IT WAS CRYSTALLIZED IN 1.4M AMMONIUM SULFATE BY HANGING DROP METHOD IN APCF REACTORS UNDER MICROGRAVITY (IML2 MISSION)., pH 7.0, vapor diffusion - hanging drop in microgravity
Crystal grow
*PLUS
Temperature: 291 K / Method: microdialysis / Details: or vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMTris-HCl1drop
360 mM1dropNaCl
41.23 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9375 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 54909 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 23.18 Å2 / Rsym value: 0.047 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.478 / % possible all: 99.6
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.478

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(ROTAVATA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB ENTRY 1HYL

1hyl


Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5345 10 %RANDOM
Rwork0.195 ---
obs0.195 54546 96.3 %-
Displacement parametersBiso mean: 22.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 0 335 3887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.521
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.261
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
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3438 666 10 %
Rwork0.3428 6225 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.261
LS refinement shell
*PLUS
Rfactor obs: 0.3428

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