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- PDB-2qn4: Structure and function study of rice bifunctional alpha-amylase/s... -

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Basic information

Entry
Database: PDB / ID: 2qn4
TitleStructure and function study of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa
ComponentsAlpha-amylase/subtilisin inhibitor
KeywordsHYDROLASE INHIBITOR / RASI / amylase inhibitor / subtilisin inhibitor / Alpha-amylase inhibitor / Protease inhibitor / Serine protease inhibitor
Function / homology
Function and homology information


alpha-amylase inhibitor activity / serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Alpha-amylase/subtilisin inhibitor
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPeng, W.Y. / Lin, Y.H. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Chen, C.J.
Citation
Journal: To be Published
Title: Structure and Function Study of Rice Bifunctional Alpha-Amylase/Subtilisin Inhibitor from Oryza Sativa
Authors: Peng, W.Y. / Lin, Y.H. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Liu, M.Y. / Chang, T. / Chen, C.J.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006
Title: Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa
Authors: Lin, Y.H. / Peng, W.Y. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Liu, M.Y. / Chang, T. / Chen, C.J.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase/subtilisin inhibitor
B: Alpha-amylase/subtilisin inhibitor


Theoretical massNumber of molelcules
Total (without water)42,8872
Polymers42,8872
Non-polymers00
Water3,567198
1
A: Alpha-amylase/subtilisin inhibitor


Theoretical massNumber of molelcules
Total (without water)21,4431
Polymers21,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-amylase/subtilisin inhibitor


Theoretical massNumber of molelcules
Total (without water)21,4431
Polymers21,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.988, 62.949, 66.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha-amylase/subtilisin inhibitor / RASI


Mass: 21443.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oryza sativa subsp. japonica (Japanese rice)
Strain: japonica cultivar-group / References: UniProt: P29421
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 20% PEG3350, 0.2M Potassium dihydrogen phosphate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2006
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 31823 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rsym value: 0.062 / Net I/σ(I): 22.5654
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5.25 / Num. unique all: 3129 / Rsym value: 0.363 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceControl Softwaredata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVA

1ava


Resolution: 1.8→30 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3076 -RANDOM
Rwork0.206 ---
all-31887 --
obs-30719 96.3 %-
Displacement parametersBiso mean: 0.16 Å2
Baniso -1Baniso -2Baniso -3
1--5.147 Å20 Å20 Å2
2---1.104 Å20 Å2
3---6.251 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.21 Å
Luzzati d res low-6 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 0 198 2622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_dihedral_angle_d27.35
X-RAY DIFFRACTIONc_improper_angle_d1.54
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.2376 281 -
Rwork0.2201 --
obs-2807 100 %

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