SAXSdb — 9zav

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

Formyl-coenzyme a transferase

Brucella melitensis 16M1W

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 50–450	Not recorded	SIN SUCCINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Index C10: 1.0M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1% PEG 200mme. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Succinate in 3 subunits was acquired from the crystallant. plate 19820 C10 drop 1, Puck: PSL-2010, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.88 Å R-free 0.225
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 50–450 Chain C； UniProt 50–450	Not recorded	SIN SUCCINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Index C10: 1.0M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1% PEG 200mme. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Succinate in 3 subunits was acquired from the crystallant. plate 19820 C10 drop 1, Puck: PSL-2010, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.88 Å R-free 0.225
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 50–450 Chain E； UniProt 50–450	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Index C10: 1.0M Succinic acid pH 7.0, 0.1M HEPES pH 7.0, 1% PEG 200mme. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Succinate in 3 subunits was acquired from the crystallant. plate 19820 C10 drop 1, Puck: PSL-2010, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.88 Å R-free 0.225

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 9ZAV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10UH Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with CoA Deposited 2026-02-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 50–450（401 aa） Chain B 50–450（401 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 3 GOL GLYCEROL × 2 ACT ACETATE ION × 2 COA COENZYME A × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Index G7: 0.20M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 20% PEG 3350. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Cocrystallization with 2mM CoA. plate 19820 G7 drop 2, Puck: PSL-1916, Cryo: 20% PEG 200 + 80% crystallant	Resolution 1.85 Å R-free 0.191
10UH Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with CoA Deposited 2026-02-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 50–450（401 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 4 GOL GLYCEROL × 2 ACT ACETATE ION × 2 COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Index G7: 0.20M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 20% PEG 3350. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Cocrystallization with 2mM CoA. plate 19820 G7 drop 2, Puck: PSL-1916, Cryo: 20% PEG 200 + 80% crystallant	Resolution 1.85 Å R-free 0.191
10UI Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with Zinc Deposited 2026-02-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 50–450（401 aa） Chain B 50–450（401 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PPX D8: 0.2M Magnesium Acetate, 0.1M MES pH 6.5, 15% PEG 6000. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. plate 19824 D8 drop 1, Puck: PSL-1911, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.34 Å R-free 0.263
10UI Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with Zinc Deposited 2026-02-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 50–450（401 aa） Chain D 50–450（401 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PPX D8: 0.2M Magnesium Acetate, 0.1M MES pH 6.5, 15% PEG 6000. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. plate 19824 D8 drop 1, Puck: PSL-1911, Cryo: 20% PEG 200 + 80% crystallant	Resolution 2.34 Å R-free 0.263

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

View Construct and Data Evidence

UniProt name	Q8YDF2_BRUME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–409； UniProt 50–450 Author chain B； PDBConstruct 9–409； UniProt 50–450 Author chain C； PDBConstruct 9–409； UniProt 50–450 Author chain D； PDBConstruct 9–409； UniProt 50–450 Author chain E； PDBConstruct 9–409； UniProt 50–450

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	9zav
Deposition date deposition_date	2025-11-19
最后修订 last_revision	2025-12-03
Structure title title	Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with succinate
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Formyl-coenzyme A transferase; 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	57.75 Å
Radius of gyration Rg (electron density) rg_electron	58.36 Å
Forward intensity I(0) i0	661050000.00
Molecular weight molecular_weight	214660.0 kDa
Excluded volume excluded_volume	268840 Å³
Envelope volume envelope_volume	407500 Å³
Hydration-shell volume shell_volume	61321 Å³
Envelope diameter envelope_diameter	198.6 Å
Shell Rg shell_rg	55.06 Å
Envelope Rg envelope_rg	57.70 Å
Shape Rg shape_rg	58.36 Å
Total Rg total_rg	58.27 Å
Total atoms total_atoms	15092
Residues n_residues	2006
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	182.2 Å
Rg (real space) rg_real	58.33 Å
Rg uncertainty (real space) rg_real_error	2.21 Å
I(0) (real space) i0_real	6.6100e+08
I(0) uncertainty (real space) i0_real_error	1.4200e+07
Rg (reciprocal space) rg_reciprocal	57.22 Å
I(0) (reciprocal space) i0_reciprocal	659900000.0000
Solution quality estimate total_estimate	0.7352
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	33.7 Å
Skewness Skewness skewness	0.402
Kurtosis Kurtosis kurtosis	-0.707
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	43110000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.578; Smooth: 0.002

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Formyl-coenzyme a transferase
Molecular weight formula_weight	44101.3 kDa
EC 编号 ec_number	2.8.3.-
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	15092

MAHHHHHHALPLAGIKVLDLSRVLAGPWATMSLADMGAEVWKIENIQGGDDTRAWSVPNYKGASTYFLCANRGKKSLALDLKSREGLEIIHELAKQADVVVENFRSGTVERLKIDYESLKALNPGIVYCSISGYGQTGPEAQRPGYDFVVQAESGLMSITGQIDGEPTRIGVAMTDIVAGMVATQSVLAALYQRKTTGLGQYIDVSLYECALNTLINVGSAHLNGGHVPARFGNAHPTVVPYQIFECSDGAFALAVGNDRQFAILCERIIDLPELAADERFKTASGRALNRAALIPPMAERFRTNTRQHWMSACLKMGVPAGQVKTVPEAFESPNVKARQVVQKLESAHLGPISLVRPAQGLKAQENAAYKAPPMLGEDSASVLGDVLGLDGNKLADLIAAGVIYQYQP

来源 Source

来源生物 organism	Brucella melitensis 16M1W
NCBI Class编号 ncbi_taxonomy_id	1143190
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	189.590 Å
Unit-cell length b length_b	189.590 Å
Unit-cell length c length_c	199.316 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	40

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	48.190 Å
R factor r_factor	0.1934
R_work r_work	0.1917
R_free r_free	0.2252

fit	/app/data/saxs_computation/za/9zav/9zav.fit
pddf	/app/data/pr_computation/za/9zav/9zav.pr.out
profile	/app/data/saxs_computation/za/9zav/9zav.dat

Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with succinate

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

Formyl-coenzyme a transferase

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)