SAXSdb — 9pav

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

6-deoxyerythronolide-B synthase

Amycolatopsis mediterranei

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 631–2179 Chain B； UniProt 631–2179 Chain C； UniProt 631–2179	Non-standard monomer：Yes (specific site not provided by mmCIF)	Antibody Fragment 1B2 Heavy Chain × 2 Antibody Fragment 1B2 Light Chain × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH) cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.22 Å

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 9PAV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11SZ Antibody (1B2) Bound Rifamycin Synthetase Module 2 Deposited 2026-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2194–3157（964 aa） Chain B 2194–3157（964 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9PAT Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Transacylation Mode Deposited 2025-06-25	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 631–2179（1549 aa） Chain B 631–2179（1549 aa） Chain C 631–2179（1549 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
9PC6 Antibody (1B2) Bound Crosslinked Rifamycin Synthetase Module 1 with a C-terminal Type II Thioesterase Deposited 2025-06-27	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 631–2180（1550 aa） Chain B 631–2180（1550 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O54666_AMYMD
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 32–1580； UniProt 631–2179 Author chain B； PDBConstruct 32–1580； UniProt 631–2179 Author chain C； PDBConstruct 32–1580； UniProt 631–2179

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	9pav
Deposition date deposition_date	2025-06-25
Structure title title	Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode
Keywords keywords	Polyketide Synthase Module, Antibody (Fab), Transferase-Immune System complex; Transferase/Immune System
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	57.18 Å
Radius of gyration Rg (electron density) rg_electron	57.11 Å
Forward intensity I(0) i0	1955450000.00
Molecular weight molecular_weight	364060.0 kDa
Excluded volume excluded_volume	453840 Å³
Envelope volume envelope_volume	725710 Å³
Hydration-shell volume shell_volume	108550 Å³
Envelope diameter envelope_diameter	194.4 Å
Shell Rg shell_rg	57.30 Å
Envelope Rg envelope_rg	55.35 Å
Shape Rg shape_rg	57.10 Å
Total Rg total_rg	57.13 Å
Total atoms total_atoms	25647
Residues n_residues	3464
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	188.9 Å
Rg (real space) rg_real	57.08 Å
Rg uncertainty (real space) rg_real_error	1.51 Å
I(0) (real space) i0_real	1.9550e+09
I(0) uncertainty (real space) i0_real_error	3.8060e+07
Rg (reciprocal space) rg_reciprocal	57.24 Å
I(0) (reciprocal space) i0_reciprocal	1956000000.0000
Solution quality estimate total_estimate	0.8827
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.0 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	88360000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.848

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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	Antibody Fragment 1B2 Heavy Chain
Molecular weight formula_weight	26447.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,G
Atom count atom_count	25647

MAEVQLVQSGGGLVQPGRSLRLSCTASGFTFGDYAMSWVRQAPGKGLEWVGFIRSKAYGGTTEYAASVKGRFTISRDDSKSIAYLQMNSLKTEDTAVYYCTRGGTLFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAALVPRGSAHHHHHHAADYKDDDDKA

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Antibody Fragment 1B2 Light Chain
Molecular weight formula_weight	25715.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,I

LFAIPLVVPFYSHSALDVVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQTPRLTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPRGAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	6-deoxyerythronolide-B synthase
Molecular weight formula_weight	175359.8 kDa
EC 编号 ec_number	2.3.1.94
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MASTDSEKVAEYLRRATLDLRAARQRIRELEGEPIAIVGMACRLPGGVASPEDLWRLVAERVDAVSEFPGDRGWDLDSLIDPDRERAGTSYVGQGGFLHDAGEFDAGFFGISPREAVAMDPQQRLLLETSWEALENAGVDPIALKGTDTGVFSGLMGQGYGSGAVAPELEGFVTTGVASSVASGRVSYVLGLEGPAVTVDTACSSSLVAMHLAAQALRQGECSMALAGGVTVMATPGSFVEFSRQRALAPDGRCKAFAAAADGTGWSEGVGVVVLERLSVARERGHRILAVLRGSAVNQDGASNGLTAPNGLSQQRVIRRALAAAGLAPSDVDVVEAHGTGTTLGDPIEAQALLATYGQERKQPLWLGSLKSNIGHAQAAAGVAGVIKMVQALRHETLPPTLHVDKPTLEVDWSAGAIELLTEARAWPRNGRPRRAGVSSFGVSGTNAHLILEEAPAEEPVAAPELPVVPLVVSARSTESLSGQAERLASLLEGDVSLTEVAGALVSRRAVLDERAVVVAGSREEAVTGLRALNTAGSGTPGKVVWVFPGQGTQWAGMGRELLAESPVFAERIAECAAALAPWIDWSLVDVLRGEGDLGRVDVLQPACFAVMVGLAAVWESVGVRPDAVVGHSQGEIAAACVSGALSLEDAAKVVALRSQAIAAELSGRGGMASVALGEDDVVSRLVDGVEVAAVNGPSSVVIAGDAHALDATLEILSGEGIRVRRVAVDYASHTRHVEDIRDTLAETLAGISAQAPAVPFYSTVTSEWVRDAGVLDGGYWYRNLRNQVRFGAAATALLEQGHTVFVEVSAHPVTVQPLSELTGDAIGTLRREDGGLRRLLASMGELFVRGIDVDWTAMVPAAGWVDLPTYAFEHRHYWLEPAEPASAGDPLLGTVVSTPGSDRLTAVAQWSRRAQPWAVDGLVPNAALVEAAIRLGDLAGTPVVGELVVDAPVVLPRRGSREVQLIVGEPGEQRRRPIEVFSREADEPWTRHAHGTLAPAAAAVPEPAAAGDATDVTVAGLRDADRYGIHPALLDAAVRTVVGDDLLPSVWTGVSLLASGATAVTVTPTATGLRLTDPAGQPVLTVESVRGTPFVAEQGTTDALFRVDWPEIPLPTAETADFLPYEATSAEATLSALQAWLADPAETRLAVVTGDCTEPGAAAIWGLVRSAQSEHPGRIVLADLDDPAVLPAVVASGEPQVRVRNGVASVPRLTRVTPRQDARPLDPEGTVLITGGTGTLGALTARHLVTAHGVRHLVLVSRRGEAPELQEELTALGASVAIAACDVADRAQLEAVLRAIPAEHPLTAVIHTAGVLDDGVVTELTPDRLATVRRPKVDAARLLDELTREADLAAFVLFSSAAGVLGNPGQAGYAAANAELDALARQRNSLDLPAVSIAWGYWATVSGMTEHLGDADLRRNQRIGMSGLPADEGMALLDAAIATGGTLVAAKFDVAALRATAKAGGPVPPLLRGLAPLPRRAAAKTASLTERLAGLAETEQAAALLDLVRRHAAEVLGHSGAESVHSGRTFKDAGFDSLTAVELRNRLAAATGLTLSPAMIFDYPKPPALADHLRAKLFGTEVRGEAPSALAGLDALEAALPEVPATEREELVQRLERMLAALRPVAQAADASGTGANPSGDDLGEAGVDELLEALGRELDGDGNSSSVDKLAAALEHHHHHH

来源 Source

来源生物 organism	Amycolatopsis mediterranei
NCBI Class编号 ncbi_taxonomy_id	33910
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	6-deoxyerythronolide-B synthase
Molecular weight formula_weight	175700.2 kDa
EC 编号 ec_number	2.3.1.94
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MASTDSEKVAEYLRRATLDLRAARQRIRELEGEPIAIVGMACRLPGGVASPEDLWRLVAERVDAVSEFPGDRGWDLDSLIDPDRERAGTSYVGQGGFLHDAGEFDAGFFGISPREAVAMDPQQRLLLETSWEALENAGVDPIALKGTDTGVFSGLMGQGYGSGAVAPELEGFVTTGVASSVASGRVSYVLGLEGPAVTVDTACSSSLVAMHLAAQALRQGECSMALAGGVTVMATPGSFVEFSRQRALAPDGRCKAFAAAADGTGWSEGVGVVVLERLSVARERGHRILAVLRGSAVNQDGASNGLTAPNGLSQQRVIRRALAAAGLAPSDVDVVEAHGTGTTLGDPIEAQALLATYGQERKQPLWLGSLKSNIGHAQAAAGVAGVIKMVQALRHETLPPTLHVDKPTLEVDWSAGAIELLTEARAWPRNGRPRRAGVSSFGVSGTNAHLILEEAPAEEPVAAPELPVVPLVVSARSTESLSGQAERLASLLEGDVSLTEVAGALVSRRAVLDERAVVVAGSREEAVTGLRALNTAGSGTPGKVVWVFPGQGTQWAGMGRELLAESPVFAERIAECAAALAPWIDWSLVDVLRGEGDLGRVDVLQPACFAVMVGLAAVWESVGVRPDAVVGHSQGEIAAACVSGALSLEDAAKVVALRSQAIAAELSGRGGMASVALGEDDVVSRLVDGVEVAAVNGPSSVVIAGDAHALDATLEILSGEGIRVRRVAVDYASHTRHVEDIRDTLAETLAGISAQAPAVPFYSTVTSEWVRDAGVLDGGYWYRNLRNQVRFGAAATALLEQGHTVFVEVSAHPVTVQPLSELTGDAIGTLRREDGGLRRLLASMGELFVRGIDVDWTAMVPAAGWVDLPTYAFEHRHYWLEPAEPASAGDPLLGTVVSTPGSDRLTAVAQWSRRAQPWAVDGLVPNAALVEAAIRLGDLAGTPVVGELVVDAPVVLPRRGSREVQLIVGEPGEQRRRPIEVFSREADEPWTRHAHGTLAPAAAAVPEPAAAGDATDVTVAGLRDADRYGIHPALLDAAVRTVVGDDLLPSVWTGVSLLASGATAVTVTPTATGLRLTDPAGQPVLTVESVRGTPFVAEQGTTDALFRVDWPEIPLPTAETADFLPYEATSAEATLSALQAWLADPAETRLAVVTGDCTEPGAAAIWGLVRSAQSEHPGRIVLADLDDPAVLPAVVASGEPQVRVRNGVASVPRLTRVTPRQDARPLDPEGTVLITGGTGTLGALTARHLVTAHGVRHLVLVSRRGEAPELQEELTALGASVAIAACDVADRAQLEAVLRAIPAEHPLTAVIHTAGVLDDGVVTELTPDRLATVRRPKVDAARLLDELTREADLAAFVLFSSAAGVLGNPGQAGYAAANAELDALARQRNSLDLPAVSIAWGYWATVSGMTEHLGDADLRRNQRIGMSGLPADEGMALLDAAIATGGTLVAAKFDVAALRATAKAGGPVPPLLRGLAPLPRRAAAKTASLTERLAGLAETEQAAALLDLVRRHAAEVLGHSGAESVHSGRTFKDAGFDXLTAVELRNRLAAATGLTLSPAMIFDYPKPPALADHLRAKLFGTEVRGEAPSALAGLDALEAALPEVPATEREELVQRLERMLAALRPVAQAADASGTGANPSGDDLGEAGVDELLEALGRELDGDGNSSSVDKLAAALEHHHHHH

来源 Source

来源生物 organism	Amycolatopsis mediterranei
NCBI Class编号 ncbi_taxonomy_id	33910
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.220 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.22 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	177509

fit	/app/data/saxs_computation/pa/9pav/9pav.fit
pddf	/app/data/pr_computation/pa/9pav/9pav.pr.out
profile	/app/data/saxs_computation/pa/9pav/9pav.dat

Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode

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

6-deoxyerythronolide-B synthase

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)