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- PDB-2yoq: Structure of FAM3B PANDER E30 construct -

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Basic information

Entry
Database: PDB / ID: 2yoq
TitleStructure of FAM3B PANDER E30 construct
ComponentsPROTEIN FAM3B
KeywordsAPOPTOSIS / 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 / MOLECULAR REPLACEMENT / Resolution: 2.35 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 6, 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)72,1996
Polymers71,9233
Non-polymers2763
Water7,422412
1
A: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0662
Polymers23,9741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0662
Polymers23,9741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0662
Polymers23,9741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.540, 86.540, 96.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.584, 0.811, -0.016), (0.811, -0.584), (-0.009, -0.013, -1)37.754, -24.817, -76.47
2given(0.401, 0.916, -0.026), (0.916, -0.401, -0.009), (-0.018, -0.02, -1)4.808, -50.132, -75.648

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Components

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


Mass: 23974.236 Da / Num. of mol.: 3
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.: 412 / 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: 3.2 Å3/Da / Density % sol: 61.13 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.35→34.47 Å / Num. obs: 33513 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 42.49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→21.64 Å / Cor.coef. Fo:Fc: 0.9457 / Cor.coef. Fo:Fc free: 0.9344 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.167
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 1690 5.05 %RANDOM
Rwork0.1583 ---
obs0.1599 33459 99.8 %-
Displacement parametersBiso mean: 34.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.1405 Å20 Å20 Å2
2---3.1405 Å20 Å2
3---6.281 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2.35→21.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 18 412 4706
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014390HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.165902HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1566SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes629HARMONIC5
X-RAY DIFFRACTIONt_it4390HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion20.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion554SEMIHARMONIC5
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_contact5052SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.42 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2846 138 4.88 %
Rwork0.2099 2692 -
all0.2135 2830 -
obs--99.8 %

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