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- PDB-1avf: ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH -

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Basic information

Entry
Database: PDB / ID: 1avf
TitleACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH
Components(GASTRICSIN) x 2
KeywordsASPARTYL PROTEASE / GASTRICSIN / ASPARTIC PROTEINASE / INTERMEDIATE / ACTIVATION / ACID
Function / homologyAspartic peptidase, N-terminal / Aspartic peptidase domain superfamily / Peptidase family A1 domain profile. / Eukaryotic and viral aspartyl proteases active site. / A1 Propeptide / Eukaryotic aspartyl protease / Gastricsin / Aspartic peptidase A1 family / Aspartic peptidase, active site / Peptidase family A1 domain ...Aspartic peptidase, N-terminal / Aspartic peptidase domain superfamily / Peptidase family A1 domain profile. / Eukaryotic and viral aspartyl proteases active site. / A1 Propeptide / Eukaryotic aspartyl protease / Gastricsin / Aspartic peptidase A1 family / Aspartic peptidase, active site / Peptidase family A1 domain / gastricsin / positive regulation of antibacterial peptide production / digestion / protein catabolic process / aspartic-type endopeptidase activity / proteolysis / extracellular space / Gastricsin
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.36 Å resolution
AuthorsKhan, A.R. / Cherney, M.M. / Tarasova, N.I. / James, M.N.G.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structural characterization of activation 'intermediate 2' on the pathway to human gastricsin.
Authors: Khan, A.R. / Cherney, M.M. / Tarasova, N.I. / James, M.N.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 16, 1997 / Release: Feb 25, 1998
RevisionDateData content typeGroupProviderType
1.0Feb 25, 1998Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: GASTRICSIN
A: GASTRICSIN
Q: GASTRICSIN
J: GASTRICSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9205
Polyers76,8974
Non-polymers231
Water8,413467
1
P: GASTRICSIN
A: GASTRICSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4723
Polyers38,4492
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2490
ΔGint (kcal/M)-22
Surface area (Å2)14430
MethodPISA
2
Q: GASTRICSIN
J: GASTRICSIN


Theoretical massNumber of molelcules
Total (without water)38,4492
Polyers38,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2450
ΔGint (kcal/M)-15
Surface area (Å2)14570
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)156.260, 50.410, 125.180
Angle α, β, γ (deg.)90.00, 117.62, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide GASTRICSIN / / PEPSINOGEN C


Mass: 2983.674 Da / Num. of mol.: 2 / Details: ASPARTIC PROTEINASE ACTIVATION INTERMEDIATE / Source: (natural) Homo sapiens (human) / Genus: Homo / Organ: STOMACH / Tissue: GASTRIC MUCOSA / References: UniProt: P20142, gastricsin
#2: Protein/peptide GASTRICSIN / / PEPSINOGEN C


Mass: 35464.930 Da / Num. of mol.: 2 / Details: ASPARTIC PROTEINASE ACTIVATION INTERMEDIATE / Source: (natural) Homo sapiens (human) / Genus: Homo / Organ: STOMACH / Tissue: GASTRIC MUCOSA / References: UniProt: P20142, gastricsin
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Formula: H2O / Water

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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: 2.5 / Density percent sol: 5 %
Crystal growpH: 7.8
Details: PROTEIN WAS CRYSTALLIZED IN 4M NA FORMATE, 100 MM BIS-TRIS-PROPANE, PH 7.8.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
14 Msodium formate1reservoir
2100 mMBis-Tris propane1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Type: EMBL/DESY, HAMBURG / Wavelength: 1
DetectorType: MARRESEARCH / Details: MIRROR / Detector: IMAGE PLATE / Collection date: Sep 1, 1996
RadiationMonochromator: GOBEL MIRRORS / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.36 Å / D resolution low: 1 Å / Number obs: 34523 / Observed criterion sigma I: 2 / Rmerge I obs: 0.066 / Rsym value: 0.117 / NetI over sigmaI: 9.2 / Redundancy: 4.3 % / Percent possible obs: 95.5
Reflection shellRmerge I obs: 0.045 / Highest resolution: 2.36 Å / Lowest resolution: 2.4 Å / MeanI over sigI obs: 3 / Rsym value: 0.303 / Redundancy: 2.5 % / Percent possible all: 80.8
Reflection shell
*PLUS
Lowest resolution: 2.4 Å / Percent possible obs: 80.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HTR
R Free selection details: RANDOM / Cross valid method: R-FREE / Sigma F: 2
Displacement parametersB iso mean: 18.54 Å2
Least-squares processR factor R free: 0.282 / R factor R work: 0.227 / R factor obs: 0.227 / Highest resolution: 2.36 Å / Lowest resolution: 2 Å / Number reflection R free: 3407 / Number reflection obs: 34523 / Percent reflection R free: 1 / Percent reflection obs: 95.3
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refine hist #LASTHighest resolution: 2.36 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5207 / Nucleic acid: 0 / Ligand: 1 / Solvent: 312 / Total: 5520
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.69
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2.0
X-RAY DIFFRACTIONx_scbond_it2.0
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints ncsWeight B iso: 1 / Weight position: 1
Refine LS shellHighest resolution: 2.36 Å / R factor R free: 0.334 / R factor R work: 0.324 / Lowest resolution: 2.39 Å / Number reflection R free: 90 / Number reflection R work: 813 / Percent reflection R free: 1 / Percent reflection obs: 8
Software
*PLUS
Name: X-PLOR / Classification: refinement
Least-squares process
*PLUS
Number reflection all: 34523 / Number reflection obs: 34124
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69

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