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- PDB-4f1p: Crystal Structure of mutant S554D for ArfGAP and ANK repeat domai... -

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Basic information

Entry
Database: PDB / ID: 4f1p
TitleCrystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1
ComponentsArf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
KeywordsPROTEIN TRANSPORT / ArfGAP domain / ANK repeat / zinc-binding module
Function / homology
Function and homology information


GTPase activator activity / recycling endosome membrane / protein transport / membrane / metal ion binding
Similarity search - Function
ArfGAP ACAP1/2/3-like / Arf GTPase activating protein / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger ...ArfGAP ACAP1/2/3-like / Arf GTPase activating protein / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger / Annexin V; domain 1 / AH/BAR domain superfamily / Ankyrin repeat-containing domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSun, F. / Pang, X. / Zhang, K. / Ma, J. / Zhou, Q.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanistic insights into regulated cargo binding by ACAP1 protein
Authors: Bai, M. / Pang, X. / Lou, J. / Zhou, Q. / Zhang, K. / Ma, J. / Li, J. / Sun, F. / Hsu, V.W.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7006
Polymers78,3772
Non-polymers3234
Water2,126118
1
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3503
Polymers39,1881
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3503
Polymers39,1881
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.561, 163.460, 41.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1 / Centaurin-beta-1 / Cnt-b1


Mass: 39188.473 Da / Num. of mol.: 2
Fragment: ArfGAP and ANK repeat domains, UNP residues 378-740
Mutation: S554D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAP1, CENTB1, KIAA0050 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15027
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.2M ammonium sulfate, 12-14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 33326 / Num. obs: 32470 / % possible obs: 97.4 % / Observed criterion σ(I): -0.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.393 / % possible all: 91.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.412 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23496 1635 5 %RANDOM
Rwork0.21714 ---
obs0.21807 30786 97.45 %-
all-31604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---2.62 Å20 Å2
3---3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 12 118 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9635181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9675496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.7824.545154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9915633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1791522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22611
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2881.52553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48823953
X-RAY DIFFRACTIONr_scbond_it0.9631422
X-RAY DIFFRACTIONr_scangle_it1.5144.51228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 95 -
Rwork0.284 1909 -
obs--91.22 %
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)
14.6079-0.42570.96674.0696-1.06733.48320.13730.0171-0.13890.3802-0.0102-0.2013-0.3460.0841-0.1270.1374-0.0320.00130.0154-0.01140.027232.405735.74165.7174
27.413-0.0947-1.54664.2655-0.0852.49590.14660.40360.3255-0.09640.05210.4414-0.0672-0.1948-0.19870.06840.00970.01910.07220.0530.08617.681749.7901-14.8788
35.41572.91591.88742.50081.18212.44170.06260.1988-0.33390.0720.0633-0.08220.0326-0.0383-0.12590.06860.00280.01310.0503-0.07670.142519.871714.2644-5.4666
45.21621.5372-1.48012.363-1.07521.89120.05920.14370.36530.09180.09650.20680.0256-0.0561-0.15570.10150.03210.02160.06030.09820.177132.330169.9925-25.53
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A407 - 524
2X-RAY DIFFRACTION2B407 - 524
3X-RAY DIFFRACTION3A569 - 697
4X-RAY DIFFRACTION4B569 - 697

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