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- PDB-2w50: N-terminal domain of human conserved dopamine neurotrophic factor... -

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Basic information

Entry
Database: PDB / ID: 2w50
TitleN-terminal domain of human conserved dopamine neurotrophic factor (CDNF)
ComponentsARMET-LIKE PROTEIN 1
KeywordsHORMONE / MANF / CDNF / SAPOSIN / SECRETED / ER STRESS / ALTERNATIVE SPLICING / GROWTH FACTOR / NEUROTROPHIC FACTOR
Function / homology
Function and homology information


dopaminergic neuron differentiation / growth factor activity / neuron projection development / endoplasmic reticulum / extracellular space
Similarity search - Function
ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / Saposin-like / NK-Lysin / SAP domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Cerebral dopamine neurotrophic factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsParkash, V. / Lindholm, P. / Peranen, J. / Kalkkinen, N. / Oksanen, E. / Saarma, M. / Leppanen, V.M. / Goldman, A.
CitationJournal: Protein Eng.Des.Sel. / Year: 2009
Title: The Structure of the Conserved Neurotrophic Factors Manf and Cdnf Explains Why They are Bifunctional.
Authors: Parkash, V. / Lindholm, P. / Peranen, J. / Kalkkinen, N. / Oksanen, E. / Saarma, M. / Leppanen, V.M. / Goldman, A.
History
DepositionDec 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / software / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARMET-LIKE PROTEIN 1
B: ARMET-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8816
Polymers23,5022
Non-polymers3804
Water2,612145
1
A: ARMET-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9413
Polymers11,7511
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ARMET-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9413
Polymers11,7511
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.300, 42.040, 51.990
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 5 / Auth seq-ID: 9 - 105 / Label seq-ID: 4 - 100

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ARMET-LIKE PROTEIN 1 / CONSERVED DOPAMINE NEUROTROPHIC FACTOR / CDNF


Mass: 11750.771 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 32-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q49AH0
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.4 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.6
Details: CRYSTALS OF CDNF AT 10-20 MG/ML WERE GROWN IN SITTING DROPS OVER A RESERVOIR SOLUTION OF 100 MM NA-ACETATE, PH 4.6, 0.2 M NH4-ACETATE AND 25-30 % MME-PEG 2000.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 110661 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0036refinement
XDSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.991 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1381 5 %RANDOM
Rwork0.209 ---
obs0.21 26056 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.73 Å2
2--0.3 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 20 145 1722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221599
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2832.0122144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7955192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.93324.68864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42915334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.471158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021112
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2332967
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.53831564
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0862632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9753580
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A388medium positional0.120.5
2B388medium positional0.120.5
1A390loose positional0.545
2B390loose positional0.545
1A388medium thermal0.872
2B388medium thermal0.872
1A390loose thermal0.8210
2B390loose thermal0.8210
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 100 -
Rwork0.284 1892 -
obs--100 %

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