SAXSdb — 3nyz

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

Indole-3-glycerol phosphate synthase

Sulfolobus solfataricus

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 1–248	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1 bis-tris, 0.2 M ammonium acetate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.51 Å R-free 0.251
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–248	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1 bis-tris, 0.2 M ammonium acetate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.51 Å R-free 0.251

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 3NYZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A53 COMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS WITH INDOLE-3-GLYCEROLPHOSPHATE AT 2.0 A RESOLUTION Deposited 1998-02-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–248（247 aa）	Not recorded	IGP INDOLE-3-GLYCEROL PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.00 Å R-free 0.212
1IGS INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS AT 2.0 A RESOLUTION Deposited 1995-08-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–248（248 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.	Resolution 2.00 Å
1JUK INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A TRIGONAL CRYSTAL FORM Deposited 1996-05-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–248（248 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.50 Å
1JUL INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A SECOND ORTHORHOMBIC CRYSTAL FORM Deposited 1996-05-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–248（248 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å
1LBF CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTASE (IGPS)WITH REDUCED 1-(O-CABOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP) Deposited 2002-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–248（247 aa）	Not recorded	137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；30% ammonium sulphate, 50 mM phosphate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.05 Å R-free 0.225
1LBL Crystal structure of indole-3-glycerol phosphate synthase (IGPS) in complex with 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate (CdRP) Deposited 2002-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–248（247 aa）	Not recorded	137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；279 K；1.2M ammonium sulphate, 50 mM potassium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.40 Å R-free 0.247
2C3Z Crystal structure of a truncated variant of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus Deposited 2005-10-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–248（222 aa） Fragment：DELTA(1-26), RESIDUES 27-248	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 30% PEG8000 0.2 M AMMONIUM SULFATE 0.1 M MES, PH 6.5	Resolution 2.80 Å
3NZ1 Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole Deposited 2010-07-15	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 1–248（248 aa）	Mutation：E51A, S81A, L83A, K110W, L131A, L157A, E159V, G178E, N180A, E210W, S211Q, L231G	3NY 5-nitro-1H-benzotriazole × 1 SO4 SULFATE ION × 6 TLA L(+)-TARTARIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.2 potassium sodium tartrate, 2M ammonium sulfate, 0.1 M sodium citrate/citric acid, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.56 Å R-free 0.210
3TC6 Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63. Deposited 2011-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–247（247 aa）	Not recorded	PO4 PHOSPHATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions Microbatch crystallization under oil；pH 5；277 K；40% PEG 400, 0.1 M Sodium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K	Resolution 1.60 Å R-free 0.198
3TC7 Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR62. Deposited 2011-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–247（247 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions Microbatch crystallization under oil；pH 5；277 K；40 % PEG 400, 0.1 M Ammonium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K	Resolution 1.50 Å R-free 0.193
4A2R Structure of the engineered retro-aldolase RA95.5-5 Deposited 2011-09-28	Different construct 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 1–245（245 aa） Fragment：TIM-BARREL FOLD, RESIDUES 1-245	Mutation：YES	3NK 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；301 K；0.1 M TRIS PH 8.5, 0.2 M NA2HPO4, 23% W/V PEG3350, 28 DEGREES CELSIUS.	Resolution 1.30 Å R-free 0.165
4A2S Structure of the engineered retro-aldolase RA95.5 Deposited 2011-09-28	Different construct 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 1–245（245 aa） Fragment：TIM-BARREL FOLD, RESIDUES 1-245	Mutation：YES	3NK 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；301 K；0.1 M HEPES KOH PH 7.6, 23% W/V PEG 3350,20 MM NA2HPO4, 28 DEG. CELSIUS.	Resolution 1.40 Å R-free 0.162
4IWW Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy Deposited 2013-01-24	Different construct 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 2–248（247 aa）	Mutation：K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；1.8 M ammonium sulfate, 5% PEG3350, pH 6.5, EVAPORATION, temperature 298K	Resolution 2.30 Å R-free 0.264
4IWW Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy Deposited 2013-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–248（247 aa）	Mutation：K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；1.8 M ammonium sulfate, 5% PEG3350, pH 6.5, EVAPORATION, temperature 298K	Resolution 2.30 Å R-free 0.264
4IX0 Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy Deposited 2013-01-24	Different construct 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 2–248（247 aa）	Mutation：K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；1.6 M ammonium sulfate, 3% PEG3350, pH 6.5, EVAPORATION, temperature 298K	Resolution 2.50 Å R-free 0.257
5AOU Structure of the engineered retro-aldolase RA95.5-8F apo Deposited 2015-09-11	Different construct 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 1–245（245 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 5 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；293 K；0.1M SODIUM ACETATE TRIHYDRATE, 2M AMMONIUM SULFATE, PH 4.6, 20DEGREE CELSIUS	Resolution 1.10 Å R-free 0.219
5K7J Structure of designed zinc binding protein ZE2 bound to Zn2+ Deposited 2016-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–248（247 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.10 M succinate 22% PEG 3350	Resolution 1.39 Å R-free 0.230
5K7J Structure of designed zinc binding protein ZE2 bound to Zn2+ Deposited 2016-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–248（247 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.10 M succinate 22% PEG 3350	Resolution 1.39 Å R-free 0.230
6NW4 Evolution of a computationally designed Kemp eliminase Deposited 2019-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–248（247 aa）	Not recorded	SO4 SULFATE ION × 4 6NT 6-NITROBENZOTRIAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate, 20 mM sodium sulfate, 43% v/v PEG 300, pH 5.6	Resolution 3.00 Å R-free 0.295

17 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRPC_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–248； UniProt 1–248 Author chain B； PDBConstruct 1–248； UniProt 1–248

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	3nyz
Deposition date deposition_date	2010-07-15
Structure title title	Crystal Structure of Kemp Elimination Catalyst 1A53-2
Keywords keywords	Tim Barrel, Kemp Elimination Enzyme, Lyase; LYASE
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	26.06 Å
Radius of gyration Rg (electron density) rg_electron	25.28 Å
Forward intensity I(0) i0	50811500.00
Molecular weight molecular_weight	56872.0 kDa
Excluded volume excluded_volume	71959 Å³
Envelope volume envelope_volume	82326 Å³
Hydration-shell volume shell_volume	27762 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	32.16 Å
Envelope Rg envelope_rg	25.37 Å
Shape Rg shape_rg	25.26 Å
Total Rg total_rg	26.12 Å
Total atoms total_atoms	4004
Residues n_residues	494
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	86.1 Å
Rg (real space) rg_real	26.15 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	5.0810e+07
I(0) uncertainty (real space) i0_real_error	6.8770e+05
Rg (reciprocal space) rg_reciprocal	26.12 Å
I(0) (reciprocal space) i0_reciprocal	50810000.0000
Solution quality estimate total_estimate	0.6606
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.463
Kurtosis Kurtosis kurtosis	-0.363
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	28440000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.964; Smooth: 0.961

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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	Indole-3-glycerol phosphate synthase
Molecular weight formula_weight	30010.5 kDa
EC 编号 ec_number	4.1.1.48
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	4338

MPRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAAYKRKSPSGLDVERDPIEYSKFMERYAVGLAIATEEKYFNGSYETLRKIASSVSIPILMWDFIVKESQIDDAYNLGADTVALIVKILTERELESLLEYARSYGMEPAIVINDENDLDIALRIGARFIEIASRDLETLEINKENQRKLISMIPSNVVKVAWQGISERNEIEELRKLGVNAFGIGSSLMRNPEKIKEFILGSIEGRGHHHHHH

来源 Source

来源生物 organism	Sulfolobus solfataricus
NCBI Class编号 ncbi_taxonomy_id	2287
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3nyza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.4 — Tryptophan biosynthesis enzymes

Domain ID domain_id	d3nyzb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.4 — Tryptophan biosynthesis enzymes

CATH v4.4 (2 domains)

Domain ID domain_id	3nyzA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3nyzB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (1)

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Unit-cell length a length_a	38.000 Å
Unit-cell length b length_b	46.310 Å
Unit-cell length c length_c	126.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.96 °
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	1.514 Å
Low-resolution limit resolution_low	36.730 Å
R factor r_factor	0.2034
R_work r_work	0.2020
R_free r_free	0.2511

fit	/app/data/saxs_computation/ny/3nyz/3nyz.fit
pddf	/app/data/pr_computation/ny/3nyz/3nyz.pr.out
profile	/app/data/saxs_computation/ny/3nyz/3nyz.dat

Crystal Structure of Kemp Elimination Catalyst 1A53-2

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

Indole-3-glycerol phosphate 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

Diffraction experiment Diffraction