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- PDB-1htr: CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT 1.62 A... -

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Basic information

Entry
Database: PDB / ID: 1htr
TitleCRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT 1.62 ANGSTROMS RESOLUTION
Components
  • GASTRICSIN
  • PROGASTRICSIN (PRO SEGMENT)
KeywordsASPARTYL PROTEASE
Function / homology
Function and homology information


gastricsin / positive regulation of antibacterial peptide production / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Helix Hairpins - #60 / Aspartic peptidase, N-terminal / A1 Propeptide / Helix Hairpins / Helix non-globular / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Special ...Helix Hairpins - #60 / Aspartic peptidase, N-terminal / A1 Propeptide / Helix Hairpins / Helix non-globular / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Special / 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 / Resolution: 1.62 Å
AuthorsMoore, S.A. / Sielecki, A.R. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal and molecular structures of human progastricsin at 1.62 A resolution.
Authors: Moore, S.A. / Sielecki, A.R. / Chernaia, M.M. / Tarasova, N.I. / James, M.N.
#1: Journal: Biochim.Biophys.Acta / Year: 1990
Title: Isolation, Crystallization and Preliminary X-Ray Diffraction Data of Human Progastricsin
Authors: Ivanov, P.K. / Chernaia, M. / Gustchina, A.E. / Pechik, I.V. / Nikonov, S.V. / Tarasova, N.I.
History
DepositionOct 21, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: PROGASTRICSIN (PRO SEGMENT)
B: GASTRICSIN


Theoretical massNumber of molelcules
Total (without water)40,6022
Polymers40,6022
Non-polymers00
Water4,504250
1
P: PROGASTRICSIN (PRO SEGMENT)
B: GASTRICSIN

P: PROGASTRICSIN (PRO SEGMENT)
B: GASTRICSIN


Theoretical massNumber of molelcules
Total (without water)81,2044
Polymers81,2044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-25 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.310, 105.310, 70.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: CIS PROLINE - PRO B 23

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Components

#1: Protein/peptide PROGASTRICSIN (PRO SEGMENT)


Mass: 5137.138 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: GASTRIC MUCOSA CELL: CHIEF CELLS / Organ: STOMACH / References: UniProt: P20142, gastricsin
#2: Protein GASTRICSIN


Mass: 35464.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: GASTRIC MUCOSA CELL: CHIEF CELLS / Organ: STOMACH / References: UniProt: P20142, gastricsin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND THE MOLECULE IS SYNTHESIZED IN THE STOMACH IN THIS INACTIVE ZYMOGEN FORM. AFTER ACTIVATION ...COMPND THE MOLECULE IS SYNTHESIZED IN THE STOMACH IN THIS INACTIVE ZYMOGEN FORM. AFTER ACTIVATION THE PROSEGMENT (RESIDUES P 1 - P 43) IS RELEASED AND THE ACTIVE MOLECULE HUMAN GASTRICSIN IS COMPOSED OF RESIDUES SER 1 - ALA 329. POSSIBLE MAIN CHAIN ALTERNATE CONFORMATION THE ELECTRON DENSITY ASSOCIATED WITH THE MAIN-CHAIN ATOMS OF RESIDUES GLN B 92 - SER B 93 AND ALA B 124 - TYR B 125 CAN ACCOMODATE TWO ALTERNATE CONFORMATIONS FOR EACH OF THOSE TWO PEPTIDES WHERE THE POSITION OF THE CORRESPONDING CARBONYL OXYGEN ATOMS OF THE MAIN-CHAIN WOULD BE FLIPPED. ONLY THE MOST PROBABLE CONFORMER OF EACH PEPTIDE IS INCLUDED IN THE CURRENT MODEL
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal grow
*PLUS
Method: seeding / PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein11
20.63 Msodium formate11
320 mMsodium-potassium phosphate 11
41.8 Msodium formate12
53-4 %(v/v)ethanol12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 50353 / % possible obs: 96 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.62 Å / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
PROLSQrefinement
TNTrefinement
RefinementResolution: 1.62→20 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.179 50353 96 %
Displacement parametersBiso mean: 27.75 Å2
Refinement stepCycle: LAST / Resolution: 1.62→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 0 250 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.022
X-RAY DIFFRACTIONp_angle_d0.0470.042
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.042
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.12
X-RAY DIFFRACTIONp_mcangle_it3.63
X-RAY DIFFRACTIONp_scbond_it2.92.5
X-RAY DIFFRACTIONp_scangle_it4.63.5
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.180.18
X-RAY DIFFRACTIONp_singtor_nbd0.240.36
X-RAY DIFFRACTIONp_multtor_nbd0.170.36
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.36
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.48
X-RAY DIFFRACTIONp_staggered_tor16.5100
X-RAY DIFFRACTIONp_orthonormal_tor21.9100
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/TNT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 50353 / Rfactor all: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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