SAXSdb — 8eul

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

Cytochrome P450-terp

Pseudomonas sp.

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 1–428	Mutation：F188A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 XGE alpha-TERPINEOL × 1 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.06 M magnesium chloride hexahyrate, 0.06 M calcium chloride dihydrate, 0.1 M sodium HEPES and MOPS (acid) pH 7.5, 20% v/v ethylene glycol, 10% v/v PEG 8000, saturating alpha-terpineol	Resolution 2.24 Å R-free 0.224

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 8EUL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CPT CRYSTAL STRUCTURE AND REFINEMENT OF CYTOCHROME P450-TERP AT 2.3 ANGSTROMS RESOLUTION Deposited 1993-11-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–428（428 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
8EUH cytochrome P450terp (cyp108A1) bound to alpha-terpineol Deposited 2022-10-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–428（428 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 XGE alpha-TERPINEOL × 2 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.06 M magnesium chloride hexahyrate, 0.06 M calcium chloride dihydrate, 0.1 M sodium HEPES and MOPS (acid) pH 7.5, 20% v/v ethylene glycol, 10% v/v PEG 8000	Resolution 2.00 Å R-free 0.210
8EUK cytochrome P450terp (cyp108A1) bound to ethylene glycol Deposited 2022-10-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–428（428 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.06 M magnesium chloride hexahyrate, 0.06 M calcium chloride dihydrate, 0.1 M sodium HEPES and MOPS (acid) pH 7.5, 20% v/v ethylene glycol, 10% v/v PEG 8000	Resolution 1.98 Å R-free 0.206

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

View Construct and Data Evidence

UniProt name	CPXL_PSESP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–448； UniProt 1–428

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	8eul
Deposition date deposition_date	2022-10-18
Structure title title	cytochrome P450terp (cyp108A1) mutant F188A bound to alpha-terpineol
Keywords keywords	monooxygenase, complex, substrate, heme, OXIDOREDUCTASE; OXIDOREDUCTASE
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	22.54 Å
Radius of gyration Rg (electron density) rg_electron	21.28 Å
Forward intensity I(0) i0	38049400.00
Molecular weight molecular_weight	47794.0 kDa
Excluded volume excluded_volume	59775 Å³
Envelope volume envelope_volume	68789 Å³
Hydration-shell volume shell_volume	26190 Å³
Envelope diameter envelope_diameter	69.7 Å
Shell Rg shell_rg	28.79 Å
Envelope Rg envelope_rg	21.55 Å
Shape Rg shape_rg	21.27 Å
Total Rg total_rg	22.19 Å
Total atoms total_atoms	3360
Residues n_residues	415
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	69.2 Å
Rg (real space) rg_real	22.41 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	3.8050e+07
I(0) uncertainty (real space) i0_real_error	4.8120e+05
Rg (reciprocal space) rg_reciprocal	22.44 Å
I(0) (reciprocal space) i0_reciprocal	38050000.0000
Solution quality estimate total_estimate	0.9056
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8404000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.984

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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	Cytochrome P450-terp
Molecular weight formula_weight	50072.5 kDa
EC 编号 ec_number	1.14.-.-
Mutation mutation	F188A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3523

MGSSHHHHHHSSGLVPRGSHMDARATIPEHIARTVILPQGYADDEVIYPAFKWLRDEQPLAMAHIEGYDPMWIATKHADVMQIGKQPGLFSNAEGSEILYDQNNEAFMRSISGGCPHVIDSLTSMDPPTHTAYRGLTLNWFQPASIRKLEENIRRIAQASVQRLLDFDGECDFMTDCALYYPLHVVMTALGVPEDDEPLMLKLTQDFAGVHEPDEQAVAAPRQSADEAARRFHETIATFYDYFNGFTVDRRSCPKDDVMSLLANSKLDGNYIDDKYINAYYVAIATAGHDTTSSSSGGAIIGLSRNPEQLALAKSDPALIPRLVDEAVRWTAPVKSFMRTALADTEVRGQNIKRGDRIMLSYPSANRDEEVFSNPDEFDITRFPNRHLGFGWGAHMCLGQHLAKLEMKIFFEELLPKLKSVELSGPPRLVATNFVGGPKNVPIRFTKA

来源 Source

来源生物 organism	Pseudomonas sp.
NCBI Class编号 ncbi_taxonomy_id	306
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	alpha-TERPINEOL
Molecular weight formula_weight	154.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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8. Citations (1)

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Unit-cell length a length_a	67.810 Å
Unit-cell length b length_b	67.810 Å
Unit-cell length c length_c	456.684 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	hexagonal

Resolution resolution	2.240 Å
Low-resolution limit resolution_low	40.930 Å
R factor r_factor	0.2007
R_work r_work	0.1995
R_free r_free	0.2239

fit	/app/data/saxs_computation/eu/8eul/8eul.fit
pddf	/app/data/pr_computation/eu/8eul/8eul.pr.out
profile	/app/data/saxs_computation/eu/8eul/8eul.dat

cytochrome P450terp (cyp108A1) mutant F188A bound to alpha-terpineol

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

Cytochrome P450-terp

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