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- PDB-4rej: Crystal structure of ginseng major latex-like protein 151 (GLP) f... -

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Basic information

Entry
Database: PDB / ID: 4rej
TitleCrystal structure of ginseng major latex-like protein 151 (GLP) from Panax ginseng. (crystal-3)
ComponentsMajor latex-like protein
KeywordsPROTEIN BINDING / major latex-like protein
Function / homology
Function and homology information


: / Pathogenesis-related protein Bet v I family / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major latex-like protein
Similarity search - Component
Biological speciesPanax ginseng (ginseng)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHong, M.K. / Kang, L.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of ginseng major latex-like protein 151 and its proposed lysophosphatidic acid-binding mechanism.
Authors: Choi, S.H. / Hong, M.K. / Kim, H.J. / Ryoo, N. / Rhim, H. / Nah, S.Y. / Kang, L.W.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major latex-like protein


Theoretical massNumber of molelcules
Total (without water)16,8921
Polymers16,8921
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.792, 61.792, 91.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Major latex-like protein


Mass: 16891.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panax ginseng (ginseng) / Gene: mlp151 / Production host: Escherichia coli (E. coli) / References: UniProt: B5THI3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Sodium citrate tribasic dehydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 440727 / Num. obs: 23046 / % possible obs: 100 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 176.5
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→30.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.813 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22103 1180 5.1 %RANDOM
Rwork0.18942 ---
obs0.19097 21829 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.152 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.69→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 0 105 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191190
X-RAY DIFFRACTIONr_bond_other_d0.0010.021113
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9391613
X-RAY DIFFRACTIONr_angle_other_deg0.89332576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.45425.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98215201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.224152
X-RAY DIFFRACTIONr_chiral_restr0.1350.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02261
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.694→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 86 -
Rwork0.228 1563 -
obs--99.52 %

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