SAXSdb — 4f1p

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 378–740	Fragment：ArfGAP and ANK repeat domains, UNP residues 378-740 Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 12-14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.235
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 378–740	Fragment：ArfGAP and ANK repeat domains, UNP residues 378-740 Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 12-14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.235

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4F1P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JUE Crystal Structure of ArfGAP and ANK repeat domain of ACAP1 Deposited 2009-09-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–740（363 aa） Fragment：ArfGAP and ANK repeat domain, residues 378-740	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.219
3JUE Crystal Structure of ArfGAP and ANK repeat domain of ACAP1 Deposited 2009-09-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 378–740（363 aa） Fragment：ArfGAP and ANK repeat domain, residues 378-740	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.219
3T9K Crystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide Deposited 2011-08-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–740（363 aa）	Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.225
3T9K Crystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide Deposited 2011-08-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 378–740（363 aa）	Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.225
4CKG Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by cryo-electron microscopy Deposited 2014-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 40 PDB declaration: 40-meric	Chain A 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain B 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain C 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain D 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50MM HEPES, PH7.4, 100MM NACL；pH 7.4；50MM HEPES, PH7.4, 100MM NACL cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 15.00 Å
4CKH Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by cryo-electron microscopy Deposited 2014-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 40 PDB declaration: 40-meric	Chain A 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain B 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain C 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain D 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50MM HEPES, PH7.4, 100MM NACL；pH 7.4；50MM HEPES, PH7.4, 100MM NACL cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4NSW Crystal structure of the BAR-PH domain of ACAP1 Deposited 2013-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–377（377 aa） Fragment：UNP residues 1-377 Chain B 1–377（377 aa） Fragment：UNP residues 1-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.2M AMMONIUM CITRATE, 10% PEG3350, 6.0MM OCTYL BETA-THIOGLUCOPYRANOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.20 Å R-free 0.266
5H3D Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 36 PDB declaration: 36-meric	Chain A 1–377（377 aa） Chain B 1–377（377 aa） Chain C 1–377（377 aa） Chain D 1–377（377 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å
5H3D Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–377（377 aa） Chain B 1–377（377 aa） Chain C 1–377（377 aa） Chain D 1–377（377 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å
5H3D Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–377（377 aa） Chain B 1–377（377 aa） Chain C 1–377（377 aa） Chain D 1–377（377 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACAP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–368； UniProt 378–740 Author chain B； PDBConstruct 6–368； UniProt 378–740

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4f1p
Deposition date deposition_date	2012-05-07
Structure title title	Crystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1
Keywords keywords	ArfGAP domain, ANK repeat, zinc-binding module, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.78 Å
Radius of gyration Rg (electron density) rg_electron	28.15 Å
Forward intensity I(0) i0	49418700.00
Molecular weight molecular_weight	53232.0 kDa
Excluded volume excluded_volume	66060 Å³
Envelope volume envelope_volume	84046 Å³
Hydration-shell volume shell_volume	26377 Å³
Envelope diameter envelope_diameter	95.8 Å
Shell Rg shell_rg	33.58 Å
Envelope Rg envelope_rg	28.14 Å
Shape Rg shape_rg	28.17 Å
Total Rg total_rg	28.63 Å
Total atoms total_atoms	3718
Residues n_residues	494
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	94.2 Å
Rg (real space) rg_real	28.90 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	4.9420e+07
I(0) uncertainty (real space) i0_real_error	7.4620e+05
Rg (reciprocal space) rg_reciprocal	28.85 Å
I(0) (reciprocal space) i0_reciprocal	49420000.0000
Solution quality estimate total_estimate	0.8719
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	9047000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.821; Smooth: 0.799

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
Molecular weight formula_weight	39188.5 kDa
Mutation mutation	S554D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3860

GPLGSGSGHLAIGSAATLGSGGMARGREPGGVGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGDLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAEAAQGQAGDETYLDIFRDFSLMASDDPEKLSRRSHDLHTL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	118

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4f1pA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	150 — Arf GTPase activating protein

Domain ID domain_id	4f1pA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	4f1pB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	150 — Arf GTPase activating protein

Domain ID domain_id	4f1pB02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (1)

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Unit-cell length a length_a	107.561 Å
Unit-cell length b length_b	163.460 Å
Unit-cell length c length_c	41.184 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2181
R_work r_work	0.2171
R_free r_free	0.2350

fit	/app/data/saxs_computation/f1/4f1p/4f1p.fit
pddf	/app/data/pr_computation/f1/4f1p/4f1p.pr.out
profile	/app/data/saxs_computation/f1/4f1p/4f1p.dat

Crystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction