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- PDB-4efv: Crystal structure of OIF from Llama seminal plasma -

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Basic information

Entry
Database: PDB / ID: 4efv
TitleCrystal structure of OIF from Llama seminal plasma
ComponentsOvulation-inducing factor (OIF)
KeywordsSIGNALING PROTEIN / HORMONE / mature OIF / beta nerve growth factor / x-ray sequencing / cysteine knot
Function / homology
Function and homology information


nerve growth factor receptor binding / nerve growth factor signaling pathway / nerve development / neuron projection morphogenesis / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / modulation of chemical synaptic transmission / synaptic vesicle / negative regulation of neuron apoptotic process / axon ...nerve growth factor receptor binding / nerve growth factor signaling pathway / nerve development / neuron projection morphogenesis / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / modulation of chemical synaptic transmission / synaptic vesicle / negative regulation of neuron apoptotic process / axon / dendrite / extracellular space / identical protein binding
Similarity search - Function
Nerve growth factor, beta subunit / 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 family profile. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...Nerve growth factor, beta subunit / 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 family profile. / 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
PHOSPHATE ION / Ovulation-inducing factor (OIF)
Similarity search - Component
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsVan Straaten, K.E. / Leduc, Y.A. / Ratto, M.H. / Valderrama, X.P. / Delbaere, T.J. / Pierson, R.A. / Adams, G.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The nerve of ovulation-inducing factor in semen.
Authors: Ratto, M.H. / Leduc, Y.A. / Valderrama, X.P. / van Straaten, K.E. / Delbaere, L.T. / Pierson, R.A. / Adams, G.P.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ovulation-inducing factor (OIF)
B: Ovulation-inducing factor (OIF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3335
Polymers26,1082
Non-polymers2253
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-43 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.930, 108.930, 49.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGchain 'A' and (resseq 10:59 or resseq 67:94 or resseq...AA10 - 5910 - 59
12GLYGLYGLYGLYchain 'A' and (resseq 10:59 or resseq 67:94 or resseq...AA67 - 9467 - 94
13GLNGLNLYSLYSchain 'A' and (resseq 10:59 or resseq 67:94 or resseq...AA96 - 11596 - 115
21GLYGLYARGARGchain 'B' and (resseq 10:59 or resseq 67:94 or resseq...BB10 - 5910 - 59
22GLYGLYGLYGLYchain 'B' and (resseq 10:59 or resseq 67:94 or resseq...BB67 - 9467 - 94
23GLNGLNLYSLYSchain 'B' and (resseq 10:59 or resseq 67:94 or resseq...BB96 - 11596 - 115

NCS oper: (Code: given
Matrix: (0.655195, -0.398284, 0.641942), (-0.4173, -0.899139, -0.131945), (0.629747, -0.181433, -0.755315)
Vector: 0.413592, 26.2202, 16.007)

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Components

#1: Protein Ovulation-inducing factor (OIF)


Mass: 13053.931 Da / Num. of mol.: 2 / Fragment: mature OIF / Source method: isolated from a natural source / Details: seminal plasma / Source: (natural) Lama glama (llama) / References: UniProt: J9PBR9*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 7.3
Details: 0.1M Tris-HCL pH 7.3, 0.7M LiSO4, 10% methanol, hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2008 / Details: mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.32→38.5 Å / Num. obs: 12822 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 49.502 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 24.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.32-2.380.7073.037328961100
2.38-2.450.6213.546905908100
2.45-2.520.5214.26620870100
2.52-2.590.3626.096664876100
2.59-2.680.2897.476340831100
2.68-2.770.2169.916261821100
2.77-2.880.1712.215930779100
2.88-30.12416.045984780100
3-3.130.08721.715389710100
3.13-3.280.06826.445282692100
3.28-3.460.04934.44997660100
3.46-3.670.04439.584889646100
3.67-3.920.03944.454275571100
3.92-4.240.03251.734173558100
4.24-4.640.02957.633777504100
4.64-5.190.02957.673414465100
5.19-5.990.02955.313026413100
5.99-7.340.02854.52571355100
7.34-10.380.02659.81891268100
10.380.02559.1896015495.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Bet

1bet


Resolution: 2.32→34.834 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8178 / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 641 5 %RANDOM
Rwork0.203 ---
obs0.2053 12820 99.95 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.011 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 104.79 Å2 / Biso mean: 48.4467 Å2 / Biso min: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1--4.5768 Å2-0 Å20 Å2
2---4.5768 Å20 Å2
3---9.1535 Å2
Refinement stepCycle: LAST / Resolution: 2.32→34.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 11 70 1717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081680
X-RAY DIFFRACTIONf_angle_d1.1762262
X-RAY DIFFRACTIONf_chiral_restr0.084260
X-RAY DIFFRACTIONf_plane_restr0.004278
X-RAY DIFFRACTIONf_dihedral_angle_d15.281590
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A767X-RAY DIFFRACTIONPOSITIONAL1.241
12B767X-RAY DIFFRACTIONPOSITIONAL1.241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.32-2.49920.32431280.254724222550
2.4992-2.75060.28291260.239523902516
2.7506-3.14830.28111280.226124372565
3.1483-3.96570.25011280.206824342562
3.9657-34.83810.20741310.174324962627

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