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- PDB-3aup: Crystal structure of Basic 7S globulin from soybean -

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Basic information

Entry
Database: PDB / ID: 3aup
TitleCrystal structure of Basic 7S globulin from soybean
ComponentsBasic 7S globulin
KeywordsPLANT PROTEIN / PEPSIN-like fold
Function / homology
Function and homology information


nutrient reservoir activity / aspartic-type endopeptidase activity / identical protein binding
Similarity search - Function
Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases ...Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsYoshizawa, T. / Shimizu, T. / Taichi, M. / Nishiuchi, Y. / Yamabe, M. / Shichijo, N. / Unzai, S. / Hirano, H. / Sato, M. / Hashimoto, H.
CitationJournal: Febs J. / Year: 2011
Title: Crystal structure of basic 7S globulin, a xyloglucan-specific endo-beta-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-beta-glucanase
Authors: Yoshizawa, T. / Shimizu, T. / Yamabe, M. / Taichi, M. / Nishiuchi, Y. / Shichijo, N. / Unzai, S. / Hirano, H. / Sato, M. / Hashimoto, H.
History
DepositionFeb 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic 7S globulin
B: Basic 7S globulin
C: Basic 7S globulin
D: Basic 7S globulin


Theoretical massNumber of molelcules
Total (without water)174,9474
Polymers174,9474
Non-polymers00
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-46 kcal/mol
Surface area54390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.240, 161.168, 84.750
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
Basic 7S globulin / SBg7S / Bg


Mass: 43736.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / References: UniProt: P13917
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M imidazol, 1.0M diammomium hydrogen phosphate, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 138568 / % possible obs: 95.6 %

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.493 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25508 6919 5 %RANDOM
Rwork0.21072 ---
obs0.21292 130736 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2---0.56 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.91→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11264 0 0 621 11885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211144
X-RAY DIFFRACTIONr_bond_other_d0.0010.027257
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.94915218
X-RAY DIFFRACTIONr_angle_other_deg2.715317675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20451473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03724.736435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92151607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9821540
X-RAY DIFFRACTIONr_chiral_restr0.1070.21755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112604
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022120
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 375 -
Rwork0.338 6974 -
obs--71.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6389-0.06840.01041.82550.00040.84520.01410.0776-0.150.0464-0.01250.08170.11220.0979-0.00160.04090.04830.01910.06990.01150.0827-18.6972-46.582.3156
21.75850.10060.15911.48950.13670.5182-0.0563-0.28530.00560.36060.0181-0.0131-0.06430.03530.03810.20090.03250.00070.12060.01650.0062-20.7655-17.1724.6251
31.55580.58550.38220.80160.08020.9696-0.07010.12450.2081-0.00240.00490.2665-0.0627-0.09480.06520.04170.0335-0.02270.07610.01880.2536-48.7901-9.7297-2.6325
41.3393-0.08290.17251.6165-0.28390.72380.1390.41320.0638-0.4179-0.22650.0332-0.060.19770.08750.30520.11320.02860.36070.08540.0412-21.0664-17.7268-22.7802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 403
2X-RAY DIFFRACTION2B6 - 401
3X-RAY DIFFRACTION3C6 - 399
4X-RAY DIFFRACTION4D6 - 400

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