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- PDB-8e0w: Crystal structure of mouse APCDD1 in P1 space group -

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Basic information

Entry
Database: PDB / ID: 8e0w
TitleCrystal structure of mouse APCDD1 in P1 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 / Resolution: 2.15 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,21713
Polymers107,5432
Non-polymers1,67411
Water3,279182
1
A: Protein APCDD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5626
Polymers53,7711
Non-polymers7915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein APCDD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6557
Polymers53,7711
Non-polymers8836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.344, 65.599, 79.686
Angle α, β, γ (deg.)74.500, 76.820, 72.230
Int Tables number1
Space group name H-MP1

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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.: 6 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.8
Details: 0.1 M magnesium acetate, 0.1 M sodium citrate, pH 5.8, 14% PEG5000 MME

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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: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.144→37.902 Å / Num. obs: 34100 / % possible obs: 91.2 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Net I/σ(I): 11.2
Reflection shellResolution: 2.144→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1 / Num. unique obs: 1705 / CC1/2: 0.886 / Rpim(I) all: 0.231 / % possible all: 59.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8E0P

8e0p


Resolution: 2.15→33.93 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 2000 5.87 %
Rwork0.179 32073 -
obs0.1814 34073 68.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.69 Å2 / Biso mean: 58.3746 Å2 / Biso min: 22.82 Å2
Refinement stepCycle: final / Resolution: 2.15→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 104 182 6981
Biso mean--79.24 45.59 -
Num. residues----827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.210.19350.25779842
2.21-2.270.2451190.30613143339
2.27-2.330.3135420.280967271420
2.33-2.410.3002760.28621207128336
2.41-2.490.29171050.28531675178050
2.49-2.590.32971310.25892123225463
2.59-2.710.30091750.26212796297183
2.71-2.860.27432050.25113281348697
2.86-3.030.26012050.23513286349198
3.03-3.270.25262070.19963323353099
3.27-3.60.22582080.16753328353699
3.6-4.120.18292060.14783326353299
4.12-5.180.1642080.12833322353099
5.19-33.930.20582080.16033341354999
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)
11.8317-0.2221-0.35353.62710.10392.95760.1014-0.13460.15380.2855-0.0516-0.4156-0.45250.1788-0.08620.2229-0.0788-0.00380.24590.01750.236912.738430.1862-12.4891
23.13420.3984-1.95632.5948-0.09534.65430.3578-0.91510.5655-0.00930.0990.1002-1.2891-0.2906-0.1020.80410.14490.18280.4779-0.02440.61280.456948.6619-8.4185
32.0634-0.11560.29132.6994-0.69973.7128-0.00690.06010.0413-0.024-0.0915-0.3313-0.21320.37570.01730.2021-0.0489-0.02250.2678-0.00450.264915.886727.3488-14.0001
41.654-0.28780.13193.7305-0.99322.7598-0.06580.0795-0.3223-0.29540.05040.09450.5639-0.23320.01670.2485-0.01390.04310.252-0.01430.2455.44216.4107-17.2184
55.10452.21310.98162.65491.81581.3727-0.7477-0.7639-0.3953-0.10230.19410.54521.3859-0.42960.26160.5891-0.030.06460.26130.09660.51375.1055-9.08440.9206
61.1246-0.1850.53513.6012-0.58723.7419-0.0103-0.009-0.0926-0.04730.00990.24390.1848-0.1308-0.01440.1917-0.0243-0.02360.28060.01110.21142.394411.8239-16.7633
73.2722-0.9417-1.70053.90590.2384.3276-0.1003-0.2490.0031-0.16790.0816-0.36670.38680.59210.01530.21550.0278-0.06030.3436-0.00620.214824.36719.1033-57.3852
84.32861.0889-1.61624.8075-1.25963.2815-0.33360.5752-0.9641-0.04970.35290.52791.3811-0.1268-0.04320.76460.01240.05240.2899-0.09210.581216.66045.3521-62.1409
92.0205-1.2323-1.10573.02460.66463.2485-0.0104-0.20420.06390.18190.0752-0.0745-0.15550.0799-0.02250.1341-0.0284-0.0330.2229-0.02920.1414.767130.235-52.3471
102.80652.28871.56477.77732.02299.71940.10530.32190.6274-0.3958-0.14950.4753-0.7561-0.86810.0330.65650.20090.11950.4080.04940.4697.859452.3596-71.4188
111.44470.0979-1.35523.310.67411.47360.2453-0.08310.308-0.2923-0.1340.2106-0.4833-0.42190.12080.27150.05270.07540.3335-0.0520.32274.290338.0638-53.6813
122.03590.73080.28741.3313-0.38051.73070.17830.2648-0.13050.0547-0.13160.34240.0067-0.29480.10620.1966-0.0361-0.0390.407-0.0360.23695.765728.603-56.1309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 170 )A50 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 198 )A171 - 198
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 281 )A199 - 281
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 373 )A282 - 373
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 411 )A374 - 411
6X-RAY DIFFRACTION6chain 'A' and (resid 412 through 467 )A412 - 467
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 156 )B50 - 156
8X-RAY DIFFRACTION8chain 'B' and (resid 157 through 218 )B157 - 218
9X-RAY DIFFRACTION9chain 'B' and (resid 219 through 373 )B219 - 373
10X-RAY DIFFRACTION10chain 'B' and (resid 374 through 400 )B374 - 400
11X-RAY DIFFRACTION11chain 'B' and (resid 401 through 438 )B401 - 438
12X-RAY DIFFRACTION12chain 'B' and (resid 439 through 466 )B439 - 466

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