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- PDB-6lh6: Crystal structure of a double headed Bowman-birk protease inhibit... -

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Basic information

Entry
Database: PDB / ID: 6lh6
TitleCrystal structure of a double headed Bowman-birk protease inhibitor protein from chickpea.
ComponentsBowman-Birk type proteinase inhibitor-like
KeywordsPROTEIN BINDING / Bowman-birk inhibitor / Chickpea / Trypsin / Protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bowman-Birk type proteinase inhibitor-like
Similarity search - Component
Biological speciesCicer arietinum (chickpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSharma, U. / Suresh, C.G.
CitationJournal: To Be Published
Title: Crystal structure of a double headed Bowman-birk protease inhibitor protein from chickpea.
Authors: Sharma, U. / Suresh, C.G.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 1.2Oct 23, 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
A: Bowman-Birk type proteinase inhibitor-like
B: Bowman-Birk type proteinase inhibitor-like


Theoretical massNumber of molelcules
Total (without water)15,8082
Polymers15,8082
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.482, 40.429, 102.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-149-

HOH

31A-157-

HOH

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Components

#1: Protein Bowman-Birk type proteinase inhibitor-like


Mass: 7904.114 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cicer arietinum (chickpea) / References: UniProt: A0A1S2XQ25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M citrate phosphate buffer pH 4.2, 40% ethanol, 5% PEG 1000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→34.3 Å / Num. obs: 30643 / % possible obs: 99.86 % / Redundancy: 2 % / Biso Wilson estimate: 10.95 Å2 / Rmerge(I) obs: 0.013 / Rpim(I) all: 0.013 / Rrim(I) all: 0.019 / Net I/σ(I): 33.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 10.5 / Num. unique obs: 2986 / CC1/2: 0.987 / Rpim(I) all: 0.066 / Rrim(I) all: 0.093 / % possible all: 99.67

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
Coot3.25model building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBI

1pbi


Resolution: 1.4→29.722 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 1556 5.08 %
Rwork0.1765 29085 -
obs0.1773 30641 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.06 Å2 / Biso mean: 18.2372 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.4→29.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 0 116 1124
Biso mean---24.95 -
Num. residues----137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.44520.21041630.18052541
1.4452-1.49680.1831470.16742583
1.4968-1.55680.17571510.16432604
1.5568-1.62760.17591410.15192586
1.6276-1.71340.16351330.1522625
1.7134-1.82070.18571330.16482644
1.8207-1.96130.18121350.16282621
1.9613-2.15860.16571400.16192658
2.1586-2.47080.22591220.16652692
2.4708-3.11250.21411500.18562693
3.1125-29.7220.19971410.22838
Refinement TLS params.Method: refined / Origin x: 6.0765 Å / Origin y: 22.4002 Å / Origin z: 10.9521 Å
111213212223313233
T0.0643 Å20.0072 Å20.0133 Å2-0.0962 Å2-0.0001 Å2--0.0744 Å2
L1.6424 °2-0.1 °2-0.5731 °2-0.8801 °20.2342 °2--1.7489 °2
S0.0395 Å °0.0496 Å °0.0691 Å °-0.0822 Å °-0.015 Å °-0.0179 Å °-0.0591 Å °0.0019 Å °-0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 71
2X-RAY DIFFRACTION1allB1 - 66
3X-RAY DIFFRACTION1allS1 - 116

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