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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(GASTRICSINProgastricsin) x 2
KeywordsASPARTYL PROTEASE / GASTRICSIN / ASPARTIC PROTEINASE / INTERMEDIATE / ACTIVATION / ACID
Function / homology
Function and homology information


gastricsin / positive regulation of antibacterial peptide production / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. ...Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
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.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polymers76,8974
Non-polymers231
Water8,413467
1
P: GASTRICSIN
A: GASTRICSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4723
Polymers38,4492
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-22 kcal/mol
Surface area14430 Å2
MethodPISA
2
Q: GASTRICSIN
J: GASTRICSIN


Theoretical massNumber of molelcules
Total (without water)38,4492
Polymers38,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-15 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
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-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.19942, 0.01342, -0.97982), (0.0186, -0.99978, -0.00991), (-0.97974, -0.01625, -0.19963)
Vector: 13.14116, -14.41568, 20.86819)

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Components

#1: Protein/peptide GASTRICSIN / Progastricsin / PEPSINOGEN C


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


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.5 Å3/Da / Density % sol: 50 %
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
IDConc.Common nameCrystal-IDSol-ID
14 Msodium formate1reservoir
2100 mMBis-Tris propane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRROR
RadiationMonochromator: GOBEL MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→100 Å / Num. obs: 34523 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.117 / Net I/σ(I): 9.2
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 3 / Rsym value: 0.303 / % possible all: 80.8
Reflection shell
*PLUS
Lowest resolution: 2.4 Å / % possible obs: 80.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HTR

1htr


Resolution: 2.36→20 Å / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 3407 10 %RANDOM
Rwork0.227 ---
obs0.227 34523 95.3 %-
Displacement parametersBiso mean: 18.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 1 312 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
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSWeight Biso : 1 / Weight position: 10
LS refinement shellResolution: 2.36→2.39 Å
RfactorNum. reflection% reflection
Rfree0.334 90 10 %
Rwork0.324 813 -
obs--80 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 34523 / Num. reflection obs: 34124
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69

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