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- PDB-3f3h: Crystal structure and anti-tumor activity of LZ-8 from the fungus... -

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Basic information

Entry
Database: PDB / ID: 3f3h
TitleCrystal structure and anti-tumor activity of LZ-8 from the fungus Ganoderma lucidium
ComponentsImmunomodulatory protein Ling Zhi-8
KeywordsANTITUMOR PROTEIN / fungal immunomodulatory protein / Ganoderma lucidium / anti-tumor activity
Function / homology
Function and homology information


regulation of immune system process / carbohydrate binding
Similarity search - Function
Fungal immunomodulatory protein Fve / Immunomodulatory protein FIP-Fve, fungal / Fungal immunomodulatory protein FIP-Fve superfamily / Fungal immunomodulatory protein Fve / : / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunomodulatory protein Ling Zhi-8
Similarity search - Component
Biological speciesGanoderma lucidum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhou, C.Z. / Huang, L. / He, Y.X. / Bao, R. / Sun, F. / Liang, C. / Liu, L.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of LZ-8 from the medicinal fungus Ganoderma lucidium
Authors: Huang, L. / Sun, F. / Liang, C. / He, Y.X. / Bao, R. / Liu, L. / Zhou, C.Z.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunomodulatory protein Ling Zhi-8
B: Immunomodulatory protein Ling Zhi-8


Theoretical massNumber of molelcules
Total (without water)25,0402
Polymers25,0402
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-29 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.190, 86.990, 92.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Immunomodulatory protein Ling Zhi-8 / LZ-8


Mass: 12519.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ganoderma lucidum (fungus) / Plasmid: p819 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P14945
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Tris, 1.75M ammonium sulfate, 6.4% polyethylene glycol 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 15951 / % possible obs: 98 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.125
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.302 / % possible all: 93.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OSY

1osy


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.809 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24552 800 5 %RANDOM
Rwork0.22096 ---
obs0.22218 15140 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.534 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å20 Å2
2--4.1 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 74 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221798
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9242458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56124.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49515267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.026158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021418
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1750.2708
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21242
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3061.51112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.52521776
X-RAY DIFFRACTIONr_scbond_it0.8073799
X-RAY DIFFRACTIONr_scangle_it1.2534.5682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 56 -
Rwork0.247 1012 -
obs--93.19 %
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)
10.3971-1.59560.890511.5021-0.58093.7611-0.1184-0.15450.16880.09980.1754-0.6970.15630.2098-0.0570.02450.04780.02960.0774-0.05630.066822.0511-3.1047-7.5047
20.8835-0.39680.22741.51980.3351.1891-0.0466-0.0018-0.1061-0.01350.04250.0740.0330.06990.00410.0445-0.0010.020.07260.00160.07427.51411.19785.6752
35.60882.60471.93416.11634.64483.5277-0.2361-0.27860.0223-0.1965-0.0780.38430.1063-0.55530.31410.12180.0370.00280.1566-0.0030.06979.127910.71314.495
41.4899-1.0482-0.17432.3170.1871.1466-0.0771-0.0435-0.0363-0.00030.0956-0.01710.10370.0399-0.01850.0511-0.00380.00190.0691-0.00610.048110.649413.84539.4195
52.8258-1.64351.447511.6084-0.73595.5784-0.1428-0.06890.0076-0.02570.1222-0.60810.01060.12210.02060.05440.00410.0520.021-0.03640.074617.89645.6215-1.9994
60.9239-0.5158-0.15180.37530.47691.78580.02570.01-0.0282-0.0005-0.06710.00470.0666-0.09290.04140.05570.0031-0.00650.0416-0.01060.077819.2505-13.1882-18.9526
710.576112.05284.526615.98753.90278.6435-0.22480.6583-0.6541-0.39340.1797-0.49570.44450.37760.04510.08510.0602-0.02050.14610.00430.011824.5293-19.3559-28.8722
81.66640.10060.19812.78290.80031.2990.0885-0.04750.09470.0215-0.0247-0.1730.01950.1116-0.06380.06110.01130.02570.0545-0.01780.043127.296-11.1545-16.8429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION2A17 - 56
3X-RAY DIFFRACTION3A57 - 68
4X-RAY DIFFRACTION4A69 - 111
5X-RAY DIFFRACTION5B3 - 16
6X-RAY DIFFRACTION6B17 - 78
7X-RAY DIFFRACTION7B79 - 84
8X-RAY DIFFRACTION8B85 - 111

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