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- PDB-8e0r: Crystal structure of mouse APCDD1 in P21 space group -

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Basic information

Entry
Database: PDB / ID: 8e0r
TitleCrystal structure of mouse APCDD1 in P21 space group
ComponentsProtein APCDD1
KeywordsSIGNALING PROTEIN / cell signaling protein / beta barrel / lipid binding protein
Function / homology
Function and homology information


regulation of odontogenesis of dentin-containing tooth / astrocyte cell migration / Wnt-protein binding / negative regulation of Wnt signaling pathway / hair follicle development / Wnt signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
APCDD1 domain / Protein APCDD1 / Adenomatosis polyposis coli down-regulated 1 / Adenomatosis polyposis coli down-regulated 1
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsHsieh, F.L. / Chang, T.H. / Gabelli, S.B. / Nathans, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein.
Authors: Hsieh, F.L. / Chang, T.H. / Gabelli, S.B. / Nathans, J.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein APCDD1
B: Protein APCDD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6497
Polymers107,5432
Non-polymers1,1065
Water6,738374
1
A: Protein APCDD1
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 54.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)54,4354
Polymers53,7711
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein APCDD1
hetero molecules


  • defined by author
  • 54.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)54,2143
Polymers53,7711
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.861, 144.128, 64.381
Angle α, β, γ (deg.)90.000, 99.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 50 - 468 / Label seq-ID: 27 - 445

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

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Components

#1: Protein Protein APCDD1 / Adenomatosis polyposis coli down-regulated 1 protein homolog


Mass: 53771.316 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 27-482)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apcdd1, Drapc1 / Plasmid: pHLsec / Production host: Homo sapiens (human) / References: UniProt: Q3U128
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 1.947→34.364 Å / Num. obs: 49930 / % possible obs: 91.1 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.057 / Net I/σ(I): 8.5
Reflection shellResolution: 1.947→2.12 Å / Rmerge(I) obs: 1.464 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2486 / CC1/2: 0.56 / Rpim(I) all: 0.58

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.82 Å34.36 Å
Translation4.82 Å34.36 Å

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8E0P

8e0p


Resolution: 1.95→34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.349 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : TLS ONLY HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 2405 4.8 %RANDOM
Rwork0.2092 ---
obs0.2111 47515 76.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.1 Å2 / Biso mean: 9.798 Å2 / Biso min: 1.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.12 Å2
2---0.01 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.95→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 70 377 7103
Biso mean--18.4 38.27 -
Num. residues----823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176305
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6639578
X-RAY DIFFRACTIONr_angle_other_deg1.1911.58614524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.545836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20621.162413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.498151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8291555
X-RAY DIFFRACTIONr_chiral_restr0.060.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021748
Refine LS restraints NCS

Ens-ID: 1 / Number: 12634 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 13 -
Rwork0.353 257 -
all-270 -
obs--5.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4046-0.05320.08260.92090.21161.4096-0.012-0.007-0.1290.0985-0.04150.03360.10120.06140.05340.0324-0.00750.0220.00950.00030.053714.91613.254116.3738
21.182-0.1785-0.14121.134-0.07960.96180.0842-0.17960.17690.0746-0.05530.0317-0.03540.0077-0.02890.0244-0.0260.00870.0385-0.02570.036139.291950.220819.8726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 480
2X-RAY DIFFRACTION2B50 - 470

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