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- PDB-1bfa: RECOMBINANT BIFUNCTIONAL HAGEMAN FACTOR/AMYLASE INHIBITOR FROM MAIZE -

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Basic information

Entry
Database: PDB / ID: 1bfa
TitleRECOMBINANT BIFUNCTIONAL HAGEMAN FACTOR/AMYLASE INHIBITOR FROM MAIZE
ComponentsBIFUNCTIONAL AMYLASE/SERINE PROTEASE INHIBITOR
KeywordsSERINE PROTEASE INHIBITOR / AMYLASE/PROTEASE BIFUNCTIONAL INHIBITOR
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal trypsin/alpha-amylase inhibitors family signature. / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trypsin/factor XIIA inhibitor
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / DIRECT PHASING / Resolution: 2.2 Å
AuthorsBehnke, C.A. / Yee, V.C. / Le Trong, I. / Pedersen, L.C. / Stenkamp, R.E. / Kim, S.S. / Reeck, G.R. / Teller, D.C.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural determinants of the bifunctional corn Hageman factor inhibitor: x-ray crystal structure at 1.95 A resolution.
Authors: Behnke, C.A. / Yee, V.C. / Trong, I.L. / Pedersen, L.C. / Stenkamp, R.E. / Kim, S.S. / Reeck, G.R. / Teller, D.C.
#1: Journal: Protein Expr.Purif. / Year: 1998
Title: The Corn Inhibitor of Activated Hageman Factor: Purification and Properties of Two Recombinant Forms of the Protein
Authors: Hazegh-Azam, M. / Kim, S.S. / Masoud, S. / Andersson, L. / White, F. / Johnson, L. / Muthukrishnan, S. / Reeck, G.
History
DepositionMay 13, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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: BIFUNCTIONAL AMYLASE/SERINE PROTEASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)14,3641
Polymers14,3641
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.120, 57.120, 80.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein BIFUNCTIONAL AMYLASE/SERINE PROTEASE INHIBITOR


Mass: 14363.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 7N-CHFI / Organ: SEED / Plasmid: PT7-7 / Species (production host): Escherichia coli / Gene (production host): 7N-CHFI / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01088
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PDB ENTRY NUMBERING REFLECTS THE MATURE PROTEIN SEQUENCE. ADDITIONAL RESIDUES FROM THE ...THE PDB ENTRY NUMBERING REFLECTS THE MATURE PROTEIN SEQUENCE. ADDITIONAL RESIDUES FROM THE EXPRESSION SYSTEM NOT VISIBLE IN ELECTRON DENSITY.

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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: 2.41 Å3/Da / Density % sol: 49 % / Description: SUBMITTED
Crystal growpH: 5.4
Details: PROTEIN WAS CRYSTALLIZED FROM 10MG/ML PROTEIN, 1% 2-PROPANOL, 1% PEG-4000, 0.1 M SODIUM CITRATE PH 5.4.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 mg/mlprotein1drop
230 %PEG4001reservoir
30.2 M1reservoirMgCl2
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 4996 / % possible obs: 77 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.1 Å2
Reflection shellResolution: 2.2→2.34 Å / % possible all: 45.6

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
PROCESSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIRECT PHASING
Starting model: PDB ENTRY 1CBA

1cba


Resolution: 2.2→50 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 515 10.3 %RANDOM
Rwork0.205 ---
obs0.205 4996 69.5 %-
Displacement parametersBiso mean: 32.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 0 14 893
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.331.5
X-RAY DIFFRACTIONx_mcangle_it4.952
X-RAY DIFFRACTIONx_scbond_it5.242
X-RAY DIFFRACTIONx_scangle_it7.862.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 43 8.2 %
Rwork0.303 479 -
obs--45.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44
LS refinement shell
*PLUS
Rfactor Rfree: 0.38

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