SAXSdb — 9zll

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

Putative conjugative transfer protein

Acinetobacter sp. NEB 394

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–552 Chain B； UniProt 2–552	Mutation：E269Q	DUF1788 domain-containing protein × 1 （A0A1L6KSM0） BREX-1 system phosphatase PglZ type A × 1 （A0A558EY06） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350	Resolution 2.74 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 2–552 Chain D； UniProt 2–552	Mutation：E269Q	DUF1788 domain-containing protein × 1 （A0A1L6KSM0） BREX-1 system phosphatase PglZ type A × 1 （A0A558EY06） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350	Resolution 2.74 Å R-free 0.248

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A1J0HS39_ACILW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–553； UniProt 2–552 Author chain B； PDBConstruct 3–553； UniProt 2–552 Author chain C； PDBConstruct 3–553； UniProt 2–552 Author chain D； PDBConstruct 3–553； UniProt 2–552

DUF1788 domain-containing protein

Acinetobacter sp. NEB 394

UniProt A0A1L6KSM0

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain G； UniProt 2–191	Not recorded	Putative conjugative transfer protein × 2 （A0A1J0HS39） BREX-1 system phosphatase PglZ type A × 1 （A0A558EY06） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350	Resolution 2.74 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 2–191	Not recorded	Putative conjugative transfer protein × 2 （A0A1J0HS39） BREX-1 system phosphatase PglZ type A × 1 （A0A558EY06） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350	Resolution 2.74 Å R-free 0.248

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A1L6KSM0_ACIHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 3–192； UniProt 2–191 Author chain G； PDBConstruct 3–192； UniProt 2–191

BREX-1 system phosphatase PglZ type A

Acinetobacter sp. NEB 394

UniProt A0A558EY06

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 2–99	Not recorded	Putative conjugative transfer protein × 2 （A0A1J0HS39） DUF1788 domain-containing protein × 1 （A0A1L6KSM0） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350	Resolution 2.74 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 2–99	Not recorded	Putative conjugative transfer protein × 2 （A0A1J0HS39） DUF1788 domain-containing protein × 1 （A0A1L6KSM0） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；250 mM NaCl, 100 mM HEPES pH 8.5, 21% PEG3350	Resolution 2.74 Å R-free 0.248

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A558EY06_9GAMM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 3–100； UniProt 2–99 Author chain H； PDBConstruct 3–100； UniProt 2–99

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	9zll
Deposition date deposition_date	2025-12-08
最后修订 last_revision	2026-04-08
Structure title title	Complex of N-terminal BrxC walker B, BrxB, and N-termianl PglZ from the Acinetobacter BREX system
Keywords keywords	Restriction, Bacteriophage, Defense, AlphaFold, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
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	49.50 Å
Radius of gyration Rg (electron density) rg_electron	49.21 Å
Forward intensity I(0) i0	1263910000.00
Molecular weight molecular_weight	293870.0 kDa
Excluded volume excluded_volume	365810 Å³
Envelope volume envelope_volume	499850 Å³
Hydration-shell volume shell_volume	83820 Å³
Envelope diameter envelope_diameter	181.8 Å
Shell Rg shell_rg	53.73 Å
Envelope Rg envelope_rg	48.45 Å
Shape Rg shape_rg	49.24 Å
Total Rg total_rg	49.29 Å
Total atoms total_atoms	20826
Residues n_residues	2703
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	170.0 Å
Rg (real space) rg_real	49.47 Å
Rg uncertainty (real space) rg_real_error	1.57 Å
I(0) (real space) i0_real	1.2640e+09
I(0) uncertainty (real space) i0_real_error	2.2170e+07
Rg (reciprocal space) rg_reciprocal	49.50 Å
I(0) (reciprocal space) i0_reciprocal	1264000000.0000
Solution quality estimate total_estimate	0.8873
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	53.1 Å
Skewness Skewness skewness	0.271
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	142300000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Putative conjugative transfer protein
Molecular weight formula_weight	63922.6 kDa
Mutation mutation	E269Q
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	21160

MGNIKELFYKPLDRAINGVVKADQDDNATVYQELDEYVVTNELEKHFRDFFQSYGTDLSDPSIANRVGVWISGFFGSGKSHFLKTLSYILANKVARDAEGNERSAAEFFDESKIRDAFIRADIGKAVSHHADVILFNIDSKASSNDDGNPILNVFLRVFNEYQGFSADHPHIAHMERHLSQKGVYERFKQAFEESSGMSWLEERDGYQFYQDDVETAISQALNLSAEAAHKWFEDSEQTFSVSVENFCQWVKEYLDSKGPQQRMLFLVDQVGQFIGSDTRLMLTLQTITENLGTICKGRAWIIVTSQADIDAVLGEMSSSKANDFSKIAGRFKTRLSLSSSNTDEVIQKRLLRKTPEAEALLRSVFEQKGDILKNQITFDRSGPTLKNYEGPDSFIHNYPFAPYHFQLVQKVFEEIRKVGATGAHLAYGERSMLDAFQMAANAIATDEVGALVPFHRFYTSVEGFLDTAVKRTIDQAGQNKTLDGFDVQMLRTLFMIRYVDIIKGTLDNLVTLSIEKIDEDKLALRKRIEESLQRLEKESLITRNGDEFLFLTHMENLYFQ

来源 Source

来源生物 organism	Acinetobacter sp. NEB 394
NCBI Class编号 ncbi_taxonomy_id	2743575
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DUF1788 domain-containing protein
Molecular weight formula_weight	21901.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G

MGSQTIHERLNQIPERILSTEFLTGQGLGNEIGFWIFDYAPEDELKVREYLHFLDGMLEKKHSQLKVVNINLLQAVVDYLAERNFIDKAIQMQKAKGDEALLKALKGPLHMDKFAPYLVSKYATNAQDIVLMTGVGSVWPLLRAHHLLNSLHSLLGHKPVVLFYPGYYDGQAMSLFGKIPSNNYYRAFRLVP

来源 Source

来源生物 organism	Acinetobacter sp. NEB 394
NCBI Class编号 ncbi_taxonomy_id	2743575
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	BREX-1 system phosphatase PglZ type A
Molecular weight formula_weight	12420.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H

MGNLSQLQQGLEQAFFHENHRIVFWYDAEQSFTEEIKALELNDVHILNMAEESSLAIKLKLELEDQQGKYLLYFPSPEPETEKDWLLDIKLYSRSFYADRLVGPR

来源 Source

来源生物 organism	Acinetobacter sp. NEB 394
NCBI Class编号 ncbi_taxonomy_id	2743575
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	334

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8. Citations (1)

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Unit-cell length a length_a	149.248 Å
Unit-cell length b length_b	114.986 Å
Unit-cell length c length_c	194.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	49.680 Å
R factor r_factor	0.2068
R_work r_work	0.2058
R_free r_free	0.2476

fit	/app/data/saxs_computation/zl/9zll/9zll.fit
pddf	/app/data/pr_computation/zl/9zll/9zll.pr.out
profile	/app/data/saxs_computation/zl/9zll/9zll.dat

Complex of N-terminal BrxC walker B, BrxB, and N-termianl PglZ from the Acinetobacter BREX system

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

Putative conjugative transfer protein

State in the Current Structure

Other States of the Same Protein in the Database

DUF1788 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

BREX-1 system phosphatase PglZ type A

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

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)