[English] 日本語
Yorodumi
- PDB-4pif: Crystal Structure of recombinant WT Banana Lectin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pif
TitleCrystal Structure of recombinant WT Banana Lectin
ComponentsRipening-associated protein
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ripening-associated protein
Similarity search - Component
Biological speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: Cell / Year: 2015
Title: Engineering a Therapeutic Lectin by Uncoupling Mitogenicity from Antiviral Activity.
Authors: Swanson, M.D. / Boudreaux, D.M. / Salmon, L. / Chugh, J. / Winter, H.C. / Meagher, J.L. / Andre, S. / Murphy, P.V. / Oscarson, S. / Roy, R. / King, S. / Kaplan, M.H. / Goldstein, I.J. / ...Authors: Swanson, M.D. / Boudreaux, D.M. / Salmon, L. / Chugh, J. / Winter, H.C. / Meagher, J.L. / Andre, S. / Murphy, P.V. / Oscarson, S. / Roy, R. / King, S. / Kaplan, M.H. / Goldstein, I.J. / Tarbet, E.B. / Hurst, B.L. / Smee, D.F. / de la Fuente, C. / Hoffmann, H.H. / Xue, Y. / Rice, C.M. / Schols, D. / Garcia, J.V. / Stuckey, J.A. / Gabius, H.J. / Al-Hashimi, H.M. / Markovitz, D.M.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ripening-associated protein
B: Ripening-associated protein
C: Ripening-associated protein
D: Ripening-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,79117
Polymers62,5944
Non-polymers1,19713
Water11,367631
1
A: Ripening-associated protein
B: Ripening-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9429
Polymers31,2972
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-14 kcal/mol
Surface area12120 Å2
MethodPISA
2
C: Ripening-associated protein
D: Ripening-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8508
Polymers31,2972
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-14 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.510, 94.492, 63.443
Angle α, β, γ (deg.)90.000, 97.470, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ripening-associated protein / lectin


Mass: 15648.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musa acuminata (dwarf banana) / Production host: Escherichia coli (E. coli) / References: UniProt: O22321
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 10-20% PEG 8000, 0.05M Potassium Phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2013 / Details: mirrors
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 63903 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.44 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.97 / Net I/av σ(I): 21.057 / Net I/σ(I): 11.8 / Num. measured all: 243152
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.733.60.30931250.91396.9
1.73-1.763.80.2631280.89797.2
1.76-1.793.80.24231680.91698.6
1.79-1.833.80.20331630.9697.7
1.83-1.873.80.1831530.96697.8
1.87-1.913.80.1531731.01998.4
1.91-1.963.80.13131601.02998.4
1.96-2.023.80.11731821.00198.5
2.02-2.073.80.10631701.06698.5
2.07-2.143.80.09731881.07598.7
2.14-2.223.80.09131891.21298.9
2.22-2.313.80.0932101.24299
2.31-2.413.80.08432231.13399.2
2.41-2.543.90.0732050.9899.1
2.54-2.73.90.06132030.92699.6
2.7-2.913.90.05332290.88899.5
2.91-3.23.80.05332411.07699.7
3.2-3.663.90.0432500.86999.8
3.66-4.613.80.03132480.66699.7
4.61-503.80.0332950.57399.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.9556 / Cor.coef. Fo:Fc free: 0.9394 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3233 5.06 %RANDOM
Rwork0.1654 ---
obs0.1669 63869 98.5 %-
Displacement parametersBiso max: 85.29 Å2 / Biso mean: 16.45 Å2 / Biso min: 4.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.5617 Å20 Å2-0.1708 Å2
2--0.0466 Å20 Å2
3---0.5151 Å2
Refine analyzeLuzzati coordinate error obs: 0.157 Å
Refinement stepCycle: final / Resolution: 1.7→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 78 631 4789
Biso mean--23.45 31.76 -
Num. residues----562
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1359SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes667HARMONIC5
X-RAY DIFFRACTIONt_it4297HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion514SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5217SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4297HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5801HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion4.39
X-RAY DIFFRACTIONt_other_torsion14.97
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2336 234 5.21 %
Rwork0.1784 4261 -
all0.1812 4495 -
obs--98.5 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more