SAXSdb — 4ber

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

PHOSPHOCHOLINE TRANSFERASE ANKX

LEGIONELLA PNEUMOPHILA

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 2–484	Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 Mutation：YES	C5P CYTIDINE-5'-MONOPHOSPHATE × 1 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；15% PEG 20000, 0.1 M TRIS PH 8.5	Resolution 2.60 Å R-free 0.239
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–484	Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 Mutation：YES	C5P CYTIDINE-5'-MONOPHOSPHATE × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；15% PEG 20000, 0.1 M TRIS PH 8.5	Resolution 2.60 Å R-free 0.239

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 4BER	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BEP Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (apo-form) Deposited 2013-03-12	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 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 Chain B 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.2 M POTASSIUM THIOCYANATE, 15-25% PEG 3350, 0.05 M HEPES PH 7.8-8.2	Resolution 3.14 Å R-free 0.286
4BES Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein in complex with cytidine monophosphate and phosphocholine Deposited 2013-03-12	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 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484	Mutation：YES	C5P CYTIDINE-5'-MONOPHOSPHATE × 2 PC PHOSPHOCHOLINE × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2 M AMMONIUM SULFATE, 30% PEG 5000 MME, 0.1 M MES PH 6.5	Resolution 2.54 Å R-free 0.259
4BET Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (inactive H229A mutant) in complex with cytidine-diphosphate-choline Deposited 2013-03-12	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 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 Chain B 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484	Mutation：YES Mutation：YES	CDC [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM × 2 SO4 SULFATE ION × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.2 M LITHIUM SULFATE, 14% PEG 4000, 0.1 M TRIS PH 7.5	Resolution 2.55 Å R-free 0.247
4BET Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (inactive H229A mutant) in complex with cytidine-diphosphate-choline Deposited 2013-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 Chain B 2–484（483 aa） Fragment：FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484	Mutation：YES Mutation：YES	CDC [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM × 2 SO4 SULFATE ION × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.2 M LITHIUM SULFATE, 14% PEG 4000, 0.1 M TRIS PH 7.5	Resolution 2.55 Å R-free 0.247
6SKU Legionella effector AnkX in complex with human Rab1b Deposited 2019-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–800（800 aa）	Mutation：C48S, C84S, G108C, C172S	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.5 M Sodium formate	Resolution 3.20 Å R-free 0.288

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANKX_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–484； UniProt 2–484 Author chain B； PDBConstruct 2–484； UniProt 2–484

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	4ber
Deposition date deposition_date	2013-03-12
Structure title title	Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein in complex with cytidine monophosphate
Keywords keywords	TRANSFERASE, TYPE IV SECRETION SYSTEM EFFECTOR; TRANSFERASE
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	36.03 Å
Radius of gyration Rg (electron density) rg_electron	35.15 Å
Forward intensity I(0) i0	177235000.00
Molecular weight molecular_weight	108620.0 kDa
Excluded volume excluded_volume	136510 Å³
Envelope volume envelope_volume	180550 Å³
Hydration-shell volume shell_volume	42244 Å³
Envelope diameter envelope_diameter	114.3 Å
Shell Rg shell_rg	42.08 Å
Envelope Rg envelope_rg	34.74 Å
Shape Rg shape_rg	35.15 Å
Total Rg total_rg	35.66 Å
Total atoms total_atoms	7682
Residues n_residues	950
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	114.7 Å
Rg (real space) rg_real	36.04 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	1.7720e+08
I(0) uncertainty (real space) i0_real_error	3.0630e+06
Rg (reciprocal space) rg_reciprocal	36.04 Å
I(0) (reciprocal space) i0_reciprocal	177200000.0000
Solution quality estimate total_estimate	0.8902
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.221
Kurtosis Kurtosis kurtosis	-0.790
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42270000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.910

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PHOSPHOCHOLINE TRANSFERASE ANKX
Molecular weight formula_weight	54889.7 kDa
EC 编号 ec_number	2.7.1.-
Mutation mutation	YES
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	7755

GVKIMPNLPGLYFLQAYPSEEIWRLFVDGRFWSKENGWRGYESREPGCLNAALESLCSIALQVEKSGEEFELSVDLIKRIHKKCGKKVEELQEKNPGELRTDEPVSFGIPAGRASIKGIEEFLSLVFLTEGGAEFGPGKAGPFGPRFDKNYFKNLNPEQIPDLAKQIYFDMCKYGHSNTNHFYLAVMKNVDVYLEKITQSYNKEIKTAETLDEKLKIIVKHIRMYEVLHPFRDANGRTFVNNLLNIPLMQQGLPPATFYEPNVFDLYSAEELVVVVKEAIFNTVEIIEQSKRKTPITLYGYHSSLEEQTKFRDMLDSPSYEKIKHMDFSDLNPEKLHLKTQKCLSSLNEQYPLHRGAIYLSDPGEIKLLLSNRNESQINQQIEQGAPPIYVGKTPAHLAVISGNMAMLDELIAKKADLSLQDYDGKTALHYAAECGNMQIMGKILKVVLSQEDAIKVLNIKDNHGKTAFHYAAEFGTPELISAL

来源 Source

来源生物 organism	LEGIONELLA PNEUMOPHILA
NCBI Class编号 ncbi_taxonomy_id	446
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CYTIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	323.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4berA02
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	4berB02
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	58.330 Å
Unit-cell length b length_b	103.560 Å
Unit-cell length c length_c	224.100 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 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	46.280 Å
R factor r_factor	0.2072
R_work r_work	0.2056
R_free r_free	0.2392

fit	/app/data/saxs_computation/be/4ber/4ber.fit
pddf	/app/data/pr_computation/be/4ber/4ber.pr.out
profile	/app/data/saxs_computation/be/4ber/4ber.dat

Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein in complex with cytidine monophosphate

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

PHOSPHOCHOLINE TRANSFERASE ANKX

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