SAXSdb — 3csm

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

CHORISMATE MUTASE

Saccharomyces cerevisiae

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 1–256 Chain B； UniProt 1–256	Not recorded	TRP TRYPTOPHAN × 2 TSA 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP, 19 % (W/V) PEG MONOMETHYLETHER 5000, 5 MM DTT, 0.15 M TRIS PH 8.0, 0.15 M SODIUM ACETATE, 16 MM TRYPTOPHAN, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.247
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–256	Not recorded	TRP TRYPTOPHAN × 2 TSA 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP, 19 % (W/V) PEG MONOMETHYLETHER 5000, 5 MM DTT, 0.15 M TRIS PH 8.0, 0.15 M SODIUM ACETATE, 16 MM TRYPTOPHAN, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.247
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–256	Not recorded	TRP TRYPTOPHAN × 2 TSA 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP, 19 % (W/V) PEG MONOMETHYLETHER 5000, 5 MM DTT, 0.15 M TRIS PH 8.0, 0.15 M SODIUM ACETATE, 16 MM TRYPTOPHAN, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.247

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 3CSM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CSM THE CRYSTAL STRUCTURE OF ALLOSTERIC CHORISMATE MUTASE AT 2.2 ANGSTROMS RESOLUTION Deposited 1994-08-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Not recorded	TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.310
2CSM TYR-BOUND T-STATE OF YEAST CHORISMATE MUTASE Deposited 1995-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa）	Not recorded	TYR TYROSINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.321
4CSM YEAST CHORISMATE MUTASE + TYR + ENDOOXABICYCLIC INHIBITOR Deposited 1997-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Not recorded	TYR TYROSINE × 2 TSA 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP, 32 % (W/V) PEG MONOMETHYLETHER 500, 4 MM DTT, 0.1 M TRIS PH 9.0, 0.1 M SODIUM CHLORIDE, 2 MM TYROSINE, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.270
4CSM YEAST CHORISMATE MUTASE + TYR + ENDOOXABICYCLIC INHIBITOR Deposited 1997-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–256（256 aa）	Not recorded	TYR TYROSINE × 2 TSA 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP, 32 % (W/V) PEG MONOMETHYLETHER 500, 4 MM DTT, 0.1 M TRIS PH 9.0, 0.1 M SODIUM CHLORIDE, 2 MM TYROSINE, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.270
4CSM YEAST CHORISMATE MUTASE + TYR + ENDOOXABICYCLIC INHIBITOR Deposited 1997-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa）	Not recorded	TYR TYROSINE × 2 TSA 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP, 32 % (W/V) PEG MONOMETHYLETHER 500, 4 MM DTT, 0.1 M TRIS PH 9.0, 0.1 M SODIUM CHLORIDE, 2 MM TYROSINE, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 2.80 Å R-free 0.270
5CSM YEAST CHORISMATE MUTASE, T226S MUTANT, COMPLEX WITH TRP Deposited 1997-07-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa）	Mutation：T226S	TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；HANGING DROP, 19 % PEG 3350, 3 MM DTT, 0.16 M SODIUM ACETATE PH 5.0, 16 MM TRYPTOPHAN, 10 MG/ML PROTEIN, vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.236

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHMU_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–256； UniProt 1–256 Author chain B； PDBConstruct 1–256； UniProt 1–256

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	3csm
Deposition date deposition_date	1997-07-10
Structure title title	STRUCTURE OF YEAST CHORISMATE MUTASE WITH BOUND TRP AND AN ENDOOXABICYCLIC INHIBITOR
Keywords keywords	;CHORISMATE PYRUVATEMUTASE, ALLOSTERIC PROTEIN, COMPLEX (ISOMERASE-PEPTIDE), TRANSITION STATE ANALOG, COMPLEX (ISOMERASE-PEPTIDE) complex ;; COMPLEX (ISOMERASE/PEPTIDE)
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	27.63 Å
Radius of gyration Rg (electron density) rg_electron	26.81 Å
Forward intensity I(0) i0	53405300.00
Molecular weight molecular_weight	59547.0 kDa
Excluded volume excluded_volume	75697 Å³
Envelope volume envelope_volume	93180 Å³
Hydration-shell volume shell_volume	29438 Å³
Envelope diameter envelope_diameter	90.8 Å
Shell Rg shell_rg	33.70 Å
Envelope Rg envelope_rg	26.72 Å
Shape Rg shape_rg	26.81 Å
Total Rg total_rg	27.56 Å
Total atoms total_atoms	4206
Residues n_residues	504
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	88.3 Å
Rg (real space) rg_real	27.64 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	5.3410e+07
I(0) uncertainty (real space) i0_real_error	7.1980e+05
Rg (reciprocal space) rg_reciprocal	27.64 Å
I(0) (reciprocal space) i0_reciprocal	53410000.0000
Solution quality estimate total_estimate	0.6796
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.5 Å
Skewness Skewness skewness	0.333
Kurtosis Kurtosis kurtosis	-0.383
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9427000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 0.075; Positv: 1.000; Valcen: 0.994; Smooth: 0.837

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CHORISMATE MUTASE
Molecular weight formula_weight	29958.5 kDa
EC 编号 ec_number	5.4.99.5
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	4206

MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLISKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKNITNSAVEEKILERLTKKAEVYGVDPTERRIERRITPEYLVKIYKEIVIPITKEVEVEYLLRRLEE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID
Molecular weight formula_weight	228.2 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3csma_
Class class	a — All alpha proteins
Fold Fold fold	a.130 — Chorismate mutase II
Superfamily Superfamily superfamily	a.130.1 — Chorismate mutase II
Family Family family	a.130.1.2 — Allosteric chorismate mutase

Domain ID domain_id	d3csmb_
Class class	a — All alpha proteins
Fold Fold fold	a.130 — Chorismate mutase II
Superfamily Superfamily superfamily	a.130.1 — Chorismate mutase II
Family Family family	a.130.1.2 — Allosteric chorismate mutase

CATH v4.4 (2 domains)

Domain ID domain_id	3csmA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	590 — Chorismate Mutase, subunit A
Homologous superfamily homologous superfamily	10 — Chorismate mutase, AroQ class superfamily, eukaryotic

Domain ID domain_id	3csmB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	590 — Chorismate Mutase, subunit A
Homologous superfamily homologous superfamily	10 — Chorismate mutase, AroQ class superfamily, eukaryotic

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8. Citations (4)

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Unit-cell length a length_a	203.500 Å
Unit-cell length b length_b	203.500 Å
Unit-cell length c length_c	128.700 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2470

fit	/app/data/saxs_computation/cs/3csm/3csm.fit
pddf	/app/data/pr_computation/cs/3csm/3csm.pr.out
profile	/app/data/saxs_computation/cs/3csm/3csm.dat

STRUCTURE OF YEAST CHORISMATE MUTASE WITH BOUND TRP AND AN ENDOOXABICYCLIC INHIBITOR

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

CHORISMATE MUTASE

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