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- PDB-4ec7: Cobra NGF in complex with lipid -

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Basic information

Entry
Database: PDB / ID: 4ec7
TitleCobra NGF in complex with lipid
ComponentsVenom nerve growth factor
KeywordsHORMONE / Cobra NGF / Unknown Lipid
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / growth factor activity / toxin activity / lipid binding / extracellular region
Similarity search - Function
Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chem-L44 / Venom nerve growth factor
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, T. / Wang, F. / Tong, Q.
CitationJournal: Faseb J. / Year: 2012
Title: Structural and functional insights into lipid-bound nerve growth factors
Authors: Tong, Q. / Wang, F. / Zhou, H.Z. / Sun, H.L. / Song, H. / Shu, Y.Y. / Gong, Y. / Zhang, W.T. / Cai, T.X. / Yang, F.Q. / Tang, J. / Jiang, T.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Venom nerve growth factor
B: Venom nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7863
Polymers26,1612
Non-polymers6251
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-21 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.120, 118.120, 87.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Venom nerve growth factor / vNGF


Mass: 13080.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: P61898
#2: Chemical ChemComp-L44 / (2S)-1-hydroxy-3-(tetradecanoyloxy)propan-2-yl docosanoate


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL44 IN 4EC7 IS UNKNOWN LIPID. THE AUTHOR DOES NOT KNOW THE COMPLETE STRUCTURE OF L44.

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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: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG mme 5000, 0.2M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 1, 2006
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→28.372 Å / Num. all: 11077 / Num. obs: 10968 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 36.11 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.372 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8301 / SU ML: 0.33 / σ(F): 1.62 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 581 5.3 %RANDOM
Rwork0.2281 ---
obs0.2304 10968 94.99 %-
all-11547 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.382 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 121.75 Å2 / Biso mean: 41.2025 Å2 / Biso min: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.1784 Å20 Å20 Å2
2---0.1784 Å2-0 Å2
3---0.3569 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 44 25 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091777
X-RAY DIFFRACTIONf_angle_d1.3582387
X-RAY DIFFRACTIONf_dihedral_angle_d20.042662
X-RAY DIFFRACTIONf_chiral_restr0.082266
X-RAY DIFFRACTIONf_plane_restr0.005299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6001-2.86160.35861420.307625302672
2.8616-3.27510.30191310.276725622693
3.2751-4.12430.2711400.211625662706
4.1243-28.37320.22791680.190227292897

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