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- PDB-9blj: Crystal structure of a serine protease inhibitor HPI from Hevea b... -

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Basic information

Entry
Database: PDB / ID: 9blj
TitleCrystal structure of a serine protease inhibitor HPI from Hevea brasiliensis
ComponentsProtease inhibitor HPI
KeywordsPLANT PROTEIN / Serine protease inhibitor
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Protease inhibitor HPI
Function and homology information
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRodriguez-Romero, A. / Hernandez-Santoyo, A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CF 2019-87163 Mexico
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Understanding the structure and function of HPI, a rubber tree serine protease inhibitor, and its interaction with subtilisin.
Authors: Terron-Hernandez, J. / Gomez-Velasco, H. / Pinzon-Yaya, L. / Hernandez-Santoyo, A. / Garcia-Ramirez, B. / Rodriguez-Romero, A.
History
DepositionApr 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease inhibitor HPI


Theoretical massNumber of molelcules
Total (without water)7,7481
Polymers7,7481
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.506, 47.506, 95.927
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-114-

HOH

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Components

#1: Protein Protease inhibitor HPI / HbPI1 / Protease inhibitor 1


Mass: 7747.798 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: PI1 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(D3) / References: UniProt: Q6XNP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe authors state that the first five residues were not observed in the electron density map due to ...The authors state that the first five residues were not observed in the electron density map due to flexibility.
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.63 % / Description: Needles
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: Solution 18 Crystal Screen 1: containing 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate at pH 6.5, and 20% w/v Polyethylene glycol 8,000
Temp details: Constant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 2, 2022 / Details: OSMIC VARIMAX OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.74→47.96 Å / Num. obs: 7132 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 22.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.014 / Rrim(I) all: 0.047 / Net I/σ(I): 23.8
Reflection shellResolution: 1.74→1.76 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 0.876 / Num. unique obs: 386 / CC1/2: 0.88 / Rpim(I) all: 0.279 / Rrim(I) all: 0.522

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Processing

Software
NameVersionClassification
PHENIX5463refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→25.25 Å / SU ML: 0.1153 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2128 674 9.51 %
Rwork0.1973 6412 -
obs0.1988 7086 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.64 Å2
Refinement stepCycle: LAST / Resolution: 1.74→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 0 0 44 540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136503
X-RAY DIFFRACTIONf_angle_d1.2349687
X-RAY DIFFRACTIONf_chiral_restr0.080984
X-RAY DIFFRACTIONf_plane_restr0.008291
X-RAY DIFFRACTIONf_dihedral_angle_d9.4283185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.870.23971300.20011231X-RAY DIFFRACTION99.85
1.87-2.060.2511310.19041254X-RAY DIFFRACTION99.86
2.06-2.360.21271320.18111257X-RAY DIFFRACTION100
2.36-2.970.23081340.22181286X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.4907128123 Å / Origin y: 11.7601010807 Å / Origin z: 2.37295768516 Å
111213212223313233
T0.221093574412 Å20.0151716489951 Å20.0126162972919 Å2-0.105525083345 Å2-0.0337973888412 Å2--0.154866501333 Å2
L2.00335888473 °20.196388677548 °20.594117029746 °2-1.94551363597 °20.136036705737 °2--4.81157262152 °2
S-0.0147356341973 Å °0.042329015578 Å °0.025949285954 Å °0.0429480132509 Å °0.10356746698 Å °-0.215428366737 Å °-0.615925536716 Å °0.133297218941 Å °-0.0788195722334 Å °
Refinement TLS groupSelection details: all

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