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- PDB-2yop: Long wavelength S-SAD structure of FAM3B PANDER -

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Basic information

Entry
Database: PDB / ID: 2yop
TitleLong wavelength S-SAD structure of FAM3B PANDER
ComponentsPROTEIN FAM3B
KeywordsAPOPTOSIS / FAM3 / DIABETES / ILEI / EMT
Function / homology
Function and homology information


insulin secretion / nuclear envelope lumen / cytokine activity / carbohydrate binding / apoptotic process / extracellular space / extracellular region
Similarity search - Function
FAM3 family / ILEI/PANDER domain / Interleukin-like EMT inducer / GG-type lectin domain profile.
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJohansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Holmberg Schiavone, L.
CitationJournal: Structure / Year: 2013
Title: Fam3B Pander and Fam3C Ilei Represent a Distinct Class of Signaling Molecules with a Non-Cytokine-Like Fold.
Authors: Johansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Schiavone, L.H.
History
DepositionOct 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / 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 / 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 / _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

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Assembly

Deposited unit
A: PROTEIN FAM3B
B: PROTEIN FAM3B
C: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7606
Polymers66,4833
Non-polymers2763
Water5,765320
1
A: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2532
Polymers22,1611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN FAM3B


Theoretical massNumber of molelcules
Total (without water)22,1611
Polymers22,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3453
Polymers22,1611
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.930, 90.440, 185.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.172, 0.983, -0.061), (0.985, 0.174, 0.021), (0.031, -0.056, -0.998)26.071, 8.689, 120.431
2given(-0.666, -0.744, 0.048), (0.746, -0.665, 0.043), (0.064, 0.998)57.858, -29.986, 31.456

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Components

#1: Protein PROTEIN FAM3B / CYTOKINE-LIKE PROTEIN 2-21 / PANCREATIC-DERIVED FACTOR / PANDER


Mass: 22161.145 Da / Num. of mol.: 3 / Fragment: RESIDUES 46-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9D309
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: LONG WAVELENGTH TWO KAPPA ANGLE S-SAD
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 2.066
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.3→30.56 Å / Num. obs: 32116 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 20.9 % / Biso Wilson estimate: 48.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 83.2

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→29.76 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9038 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.268 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.201
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1619 5.05 %RANDOM
Rwork0.1848 ---
obs0.187 32057 97.02 %-
Displacement parametersBiso mean: 46.38 Å2
Baniso -1Baniso -2Baniso -3
1--14.2115 Å20 Å20 Å2
2--5.9724 Å20 Å2
3---8.2391 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 18 320 4577
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014353HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.195851HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes624HARMONIC5
X-RAY DIFFRACTIONt_it4353HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion19.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion550SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4933SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2707 108 4.88 %
Rwork0.2253 2105 -
all0.2276 2213 -
obs--97.02 %

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