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- PDB-4az9: Crystal structure of phox homology domain of human sorting nexin 24 -

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Basic information

Entry
Database: PDB / ID: 4az9
TitleCrystal structure of phox homology domain of human sorting nexin 24
ComponentsSORTING NEXIN-24
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


phosphatidylinositol phosphate binding / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / cytoplasmic vesicle membrane / protein transport
Similarity search - Function
: / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.75 Å
AuthorsOberholzer, A.E. / Kiyani, W. / Krojer, T. / Shrestha, L. / von Delft, F. / Froese, D.S. / Chaikuad, A. / Raynor, J. / Arrowsmith, C. / Edwards, A. ...Oberholzer, A.E. / Kiyani, W. / Krojer, T. / Shrestha, L. / von Delft, F. / Froese, D.S. / Chaikuad, A. / Raynor, J. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Phox Homology Domain of Human Sorting Nexin 24
Authors: Oberholzer, A.E. / Kiyani, W. / Krojer, T. / Shrestha, L. / von Delft, F. / Froese, D.S. / Chaikuad, A. / Raynor, J. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionJun 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Structure summary
Revision 1.2Nov 20, 2013Group: Derived calculations / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
A: SORTING NEXIN-24
B: SORTING NEXIN-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1444
Polymers31,0202
Non-polymers1242
Water4,648258
1
A: SORTING NEXIN-24
hetero molecules

B: SORTING NEXIN-24


Theoretical massNumber of molelcules
Total (without water)31,1444
Polymers31,0202
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area1640 Å2
ΔGint-3.1 kcal/mol
Surface area14040 Å2
MethodPISA
2
B: SORTING NEXIN-24

A: SORTING NEXIN-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1444
Polymers31,0202
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area1640 Å2
ΔGint-3.1 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.526, 54.241, 122.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SORTING NEXIN-24


Mass: 15509.854 Da / Num. of mol.: 2 / Fragment: PHOX HOMOLOGY DOMAIN, RESIDUES 160-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9Y343
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.33 Å3/Da / Density % sol: 47.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→122.68 Å / Num. obs: 30020 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.75→122.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.213 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20473 1521 5.1 %RANDOM
Rwork0.18074 ---
obs0.18195 28447 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→122.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 8 258 2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021985
X-RAY DIFFRACTIONr_bond_other_d0.0050.021375
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9642699
X-RAY DIFFRACTIONr_angle_other_deg1.2573.0013360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96823.9898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5261511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212185
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02418
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 109 -
Rwork0.282 1888 -
obs--100 %
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)
110.19258.28651.539827.39112.459510.4013-0.0255-0.5698-0.40740.0469-0.243-0.47910.29920.63670.26840.01190.03770.00470.16330.01260.0422-13.301133.5764-41.343
21.0481-0.5378-0.40594.12981.83883.11530.01140.05360.0299-0.1997-0.0117-0.1762-0.18670.24710.00030.09380.00710.01530.06070.00490.0553-14.61096.4602-56.4592
31.5125-0.1314-1.62771.712.14669.24090.00510.0009-0.0960.0806-0.12420.04030.16650.16340.11910.1060.0044-0.00890.05890.00150.0763-18.01872.4699-42.7025
40.57890.25480.38990.97641.22644.47460.0409-0.0324-0.02920.0751-0.06230.05990.1788-0.23980.02150.069-0.00620.01030.0726-0.01020.0756-24.1039-0.541-49.1081
50.7980.19960.49832.46451.95254.2218-0.00280.0457-0.04670.0736-0.08210.2283-0.1561-0.31540.0850.09190.0524-0.00150.0943-0.01360.068-24.88148.468-52.1911
65.1908-0.1999-1.64881.5050.5656.00090.0666-0.2465-0.0270.1856-0.0157-0.1344-0.4990.4126-0.05090.1695-0.0468-0.01330.0464-0.00610.0188-15.038113.9351-41.4981
712.6381.7352-3.49682.6766-2.68169.75810.37990.06880.77350.29240.07690.039-0.6201-0.1177-0.45680.05780.02450.01850.04860.0390.1812-34.45317.4049-14.144
82.9376-1.42910.88560.7926-0.51651.0252-0.067-0.0227-0.15170.07930.05970.10520.1275-0.01370.00740.09550.01860.00480.0950.01460.111-13.69043.7863-10.2994
91.76630.28462.9661.3219-2.03189.9492-0.06530.1997-0.0566-0.1541-0.078-0.13840.17180.48770.14330.05840.01980.01730.1681-0.0040.0657-8.72087.0131-24.7308
103.4676-0.6683.8720.7093-0.13395.5413-0.03830.11360.0362-0.11490.0503-0.1272-0.08820.2638-0.01210.0465-0.0320.01680.13430.02440.0907-2.377512.3161-17.6767
112.9873-1.20782.09961.1256-1.48783.1671-0.04260.04710.1509-0.0086-0.0167-0.0628-0.24760.20750.05930.0891-0.0199-0.00370.1010.01230.104-10.471914.3779-14.2976
121.6981.1626-0.17094.7683-1.00066.34250.00740.1821-0.1083-0.1724-0.00670.03990.0314-0.1749-0.00070.04850.0053-0.00760.1119-0.00640.0592-20.49159.1936-24.8803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 0
2X-RAY DIFFRACTION2A1 - 39
3X-RAY DIFFRACTION3A40 - 50
4X-RAY DIFFRACTION4A51 - 70
5X-RAY DIFFRACTION5A71 - 87
6X-RAY DIFFRACTION6A88 - 105
7X-RAY DIFFRACTION7B-8 - 0
8X-RAY DIFFRACTION8B1 - 39
9X-RAY DIFFRACTION9B40 - 50
10X-RAY DIFFRACTION10B51 - 70
11X-RAY DIFFRACTION11B71 - 87
12X-RAY DIFFRACTION12B88 - 102

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