SAXSdb — 2c2n

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

MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE

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 60–375	Fragment：RESIDUES 60-375	SO4 SULFATE ION × 6 AE4 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL × 1 DXE 1,2-DIMETHOXYETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；32%PEG4000, 0.25M LI2SO4, 100MM TRIS-HCL, PH8.5, SITTING DROP, 293 K, pH 8.50	Resolution 1.55 Å R-free 0.218
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 60–375	Fragment：RESIDUES 60-375	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 AE3 2-(2-ETHOXYETHOXY)ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；32%PEG4000, 0.25M LI2SO4, 100MM TRIS-HCL, PH8.5, SITTING DROP, 293 K, pH 8.50	Resolution 1.55 Å R-free 0.218

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 2C2N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8CSP Human mitochondrial small subunit assembly intermediate (State A) Deposited 2022-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric	Chain 8 1–390（390 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 SAM S-ADENOSYLMETHIONINE × 1 K POTASSIUM ION × 4 MG MAGNESIUM ION × 28 FES FE2/S2 (INORGANIC) CLUSTER × 2 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
8CSQ Human mitochondrial small subunit assembly intermediate (State B) Deposited 2022-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric	Chain 8 1–390（390 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 SAM S-ADENOSYLMETHIONINE × 1 K POTASSIUM ION × 4 MG MAGNESIUM ION × 27 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
8CSR Human mitochondrial small subunit assembly intermediate (State C) Deposited 2022-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric	Chain 8 1–390（390 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 SAM S-ADENOSYLMETHIONINE × 1 K POTASSIUM ION × 5 MG MAGNESIUM ION × 31 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
8CSS Human mitochondrial small subunit assembly intermediate (State D) Deposited 2022-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric	Chain 8 1–390（390 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 SAM S-ADENOSYLMETHIONINE × 1 K POTASSIUM ION × 7 MG MAGNESIUM ION × 32 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.36 Å

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

View Construct and Data Evidence

UniProt name	FABD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–339； UniProt 60–375 Author chain B； PDBConstruct 24–339； UniProt 60–375

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	2c2n
Deposition date deposition_date	2005-09-29
Structure title title	Structure of human mitochondrial malonyltransferase
Keywords keywords	FATTY ACID SYNTHASE, LIPID SYNTHESIS, MITOCHONDRION TRANSFERASE, 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	29.65 Å
Radius of gyration Rg (electron density) rg_electron	29.02 Å
Forward intensity I(0) i0	78205100.00
Molecular weight molecular_weight	69214.0 kDa
Excluded volume excluded_volume	86496 Å³
Envelope volume envelope_volume	106010 Å³
Hydration-shell volume shell_volume	31101 Å³
Envelope diameter envelope_diameter	94.8 Å
Shell Rg shell_rg	35.76 Å
Envelope Rg envelope_rg	28.90 Å
Shape Rg shape_rg	29.05 Å
Total Rg total_rg	29.58 Å
Total atoms total_atoms	4853
Residues n_residues	625
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	95.7 Å
Rg (real space) rg_real	29.72 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	7.8210e+07
I(0) uncertainty (real space) i0_real_error	1.0980e+06
Rg (reciprocal space) rg_reciprocal	29.69 Å
I(0) (reciprocal space) i0_reciprocal	78200000.0000
Solution quality estimate total_estimate	0.8890
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10730000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.926

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
Molecular weight formula_weight	37654.4 kDa
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	5479

MHHHHHHSSGVDLGTENLYFQSMGQCSVLLFPGQGSQVVGMGRGLLNYPRVRELYAAARRVLGYDLLELSLHGPQETLDRTVHCQPAIFVASLAAVEKLHHLQPSVIENCVAAAGFSVGEFAALVFAGAMEFAEGLYAVKIRAEAMQEASEAVPSGMLSVLGQPQSKFNFACLEAREHCKSLGIENPVCEVSNYLFPDCRVISGHQEALRFLQKNSSKFHFRRTRMLPVSGAFHTRLMEPAVEPLTQALKAVDIKKPLVSVYSNVHGHRYRHPGHIHKLLAQQLVSPVKWEQTMHAIYERKKGRGFPQTFEVGPGRQLGAILKSCNMQAWKSYSAVDVL

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-DIMETHOXYETHANE
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	2-(2-ETHOXYETHOXY)ETHANOL
Molecular weight formula_weight	134.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	575

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2c2nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	366 — Malonyl-Coenzyme A Acyl Carrier Protein; domain 2
Homologous superfamily homologous superfamily	10 — Malonyl-Coenzyme A Acyl Carrier Protein, domain 2

Domain ID domain_id	2c2nA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	250 — Malonyl-CoA ACP transacylase, ACP-binding

Domain ID domain_id	2c2nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	366 — Malonyl-Coenzyme A Acyl Carrier Protein; domain 2
Homologous superfamily homologous superfamily	10 — Malonyl-Coenzyme A Acyl Carrier Protein, domain 2

Domain ID domain_id	2c2nB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	250 — Malonyl-CoA ACP transacylase, ACP-binding

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8. Citations (1)

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Unit-cell length a length_a	52.573 Å
Unit-cell length b length_b	84.828 Å
Unit-cell length c length_c	74.565 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	74.330 Å
R factor r_factor	0.1790
R_work r_work	0.1780
R_free r_free	0.2180

fit	/app/data/saxs_computation/c2/2c2n/2c2n.fit
pddf	/app/data/pr_computation/c2/2c2n/2c2n.pr.out
profile	/app/data/saxs_computation/c2/2c2n/2c2n.dat

Structure of human mitochondrial malonyltransferase