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- PDB-1h34: Crystal structure of lima bean trypsin inhibitor -

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Basic information

Entry
Database: PDB / ID: 1h34
TitleCrystal structure of lima bean trypsin inhibitor
ComponentsBOWMAN-BIRK TYPE PROTEINASE INHIBITOR
KeywordsINHIBITOR / BOWMAN-BIRK-TYPE PROTEINASE INHIBITOR / SERINE 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 / Bowman-Birk serine protease inhibitors family signature. / 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
Similarity search - Component
Biological speciesPHASEOLUS LUNATUS (lima bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.04 Å
AuthorsDebreczeni, J.E. / Bunkoczi, G. / Girmann, B. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: In-House Phase Determination of the Lima Bean Trypsin Inhibitor: A Low-Resolution Sulfur-Sad Case
Authors: Debreczeni, J.E. / Bunkoczi, G. / Girmann, B. / Sheldrick, G.M.
History
DepositionAug 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)9,0441
Polymers9,0441
Non-polymers00
Water1,40578
1
A: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR

A: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)18,0882
Polymers18,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555-x+1/2,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)109.157, 109.157, 109.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2015-

HOH

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Components

#1: Protein BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Mass: 9043.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PHASEOLUS LUNATUS (lima bean) / Organ: SEED / References: UniProt: P01056
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE BOWMAN-BIRK SERINE PROTEASE INHIBITOR FAMILY.

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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: 6.02 Å3/Da / Density % sol: 79.5 % / Description: PHASED USING IN-HOUSE SULFUR-SAD DATA
Crystal growpH: 7.5 / Details: 0.6 M K,NA-TARTRATE, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.6 Mpotassium sodium tartrate tetrahydrate1reservoir
30.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8431
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8431 Å / Relative weight: 1
ReflectionResolution: 2.04→77.19 Å / Num. obs: 13776 / % possible obs: 98.5 % / Redundancy: 6.33 % / Rmerge(I) obs: 0.0567 / Net I/σ(I): 12.43
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.2975 / Mean I/σ(I) obs: 3.58 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 2.05 Å / Redundancy: 6.3 % / Num. measured all: 88491 / Rmerge(I) obs: 0.0567
Reflection shell
*PLUS
Highest resolution: 2.05 Å / % possible obs: 96.1 % / Redundancy: 3.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
SHELXL-97refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.04→10 Å / Num. parameters: 2007 / Num. restraintsaints: 1747 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE FIRST 15 AND THE LAST 11 RESIDUES ARE NOT VISIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 676 5 %RANDOM
all0.2529 13638 --
obs0.2534 -98.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum non hydrogen: 500.83
Refinement stepCycle: LAST / Resolution: 2.04→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms424 0 0 78 502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0315
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.097
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.2302 / Highest resolution: 2.05 Å / Lowest resolution: 77.19 Å / Rfactor Rfree: 0.2497
Solvent computation
*PLUS
Displacement parameters
*PLUS

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