SAXSdb — 4odo

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

Peptidyl-prolyl cis-trans isomerase SlyD

Thermus thermophilus

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 1–149	Not recorded	MG MAGNESIUM ION × 3 CL CHLORIDE ION × 1 FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.204
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–149	Not recorded	CL CHLORIDE ION × 1 FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.204
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–149	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.204

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 4ODO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CGM Crystal structure of thermophilic SlyD Deposited 2008-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–149（149 aa）	Not recorded	SCN THIOCYANATE ION × 6 NI NICKEL (II) ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；286 K；60mg/ml protein, 1:1 mixing, 2M Ammonium sulfate, 2% PEG 400, 1% Thiocyanate, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 2.41 Å R-free 0.226
3CGM Crystal structure of thermophilic SlyD Deposited 2008-03-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–149（149 aa）	Not recorded	SCN THIOCYANATE ION × 36 NI NICKEL (II) ION × 6 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；286 K；60mg/ml protein, 1:1 mixing, 2M Ammonium sulfate, 2% PEG 400, 1% Thiocyanate, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 2.41 Å R-free 0.226
3CGN Crystal Structure of thermophilic SlyD Deposited 2008-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–149（149 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；286 K；100mM MES, pH6.5, 1.6M Na/K-Tartrate, 26mg/ml, 1:1 mixing, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 2.70 Å R-free 0.257
3CGN Crystal Structure of thermophilic SlyD Deposited 2008-03-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；286 K；100mM MES, pH6.5, 1.6M Na/K-Tartrate, 26mg/ml, 1:1 mixing, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 2.70 Å R-free 0.257
3LUO Crystal Structure and functional characterization of the thermophilic prolyl isomerase and chaperone SlyD Deposited 2010-02-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；10MG/ML N-SUC-ALA-LEU-PRO-PHE-PNA, 2M AMMONIUM SULFATE, 5 % PEG 400, 100MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.55 Å R-free 0.235
3LUO Crystal Structure and functional characterization of the thermophilic prolyl isomerase and chaperone SlyD Deposited 2010-02-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–149（149 aa）	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；10MG/ML N-SUC-ALA-LEU-PRO-PHE-PNA, 2M AMMONIUM SULFATE, 5 % PEG 400, 100MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.55 Å R-free 0.235
4ODK Structure of SlyD from Thermus thermophilus in complex with T1 peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；13.2% PEG1500, 0.1 M HEPES, pH 7.5, 0.05 M sodium chloride, 11% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.40 Å R-free 0.167
4ODL Structure of SlyD from Thermus thermophilus in complex with S2 peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.92 Å R-free 0.224
4ODL Structure of SlyD from Thermus thermophilus in complex with S2 peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.92 Å R-free 0.224
4ODM Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；19% PEG3350, 8% Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.208
4ODM Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1 ACT ACETATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；19% PEG3350, 8% Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.208
4ODM Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；19% PEG3350, 8% Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.208
4ODM Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；19% PEG3350, 8% Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.208
4ODN Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide Deposited 2014-01-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG6000, 0.1 M citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.198
4ODP Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide Deposited 2014-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Fragment：SEE REMARK 999 Chain A 126–149（24 aa） Fragment：SEE REMARK 999	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28% PEG400, 0.1 M HEPES, pH 7.5, 0.2 M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.202
4ODQ Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide Deposited 2014-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Fragment：SEE REMARK 999 Chain A 126–149（24 aa） Fragment：SEE REMARK 999	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；25% PEG6000, 0.1 M Tris-HCl, pH 8.0, 0.2 M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.213
4ODR Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506 Deposited 2014-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–64（64 aa） Fragment：SEE REMARK 999 Chain A 126–149（24 aa） Fragment：SEE REMARK 999	Not recorded	FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 ZN ZINC ION × 2 CL CHLORIDE ION × 1 GOL GLYCEROL × 4 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG6000, 0.1 M sodium acetate, pH 5.0, 0.2 M zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.93 Å R-free 0.170
4ODR Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506 Deposited 2014-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–64（64 aa） Fragment：SEE REMARK 999 Chain B 126–149（24 aa） Fragment：SEE REMARK 999	Not recorded	FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；20% PEG6000, 0.1 M sodium acetate, pH 5.0, 0.2 M zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.93 Å R-free 0.170
7OXG ttSlyD FKBP domain with M8A pseudo-wild-type S2 peptide Deposited 2021-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain A 126–149（24 aa）	Mutation：Deletion of IF domain Mutation：Deletion of IF domain	CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 5.5；292.15 K；Bis-Tris, PEG 3350	Resolution 2.00 Å R-free 0.247
7OXG ttSlyD FKBP domain with M8A pseudo-wild-type S2 peptide Deposited 2021-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–64（64 aa） Chain B 126–149（24 aa）	Mutation：Deletion of IF domain Mutation：Deletion of IF domain	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 5.5；292.15 K；Bis-Tris, PEG 3350	Resolution 2.00 Å R-free 0.247
7OXH ttSlyD with pseudo-wild-type S2 peptide Deposited 2021-06-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 NI NICKEL (II) ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 6.5；292.15 K；Sodium cacodylate, PEG 200	Resolution 1.70 Å R-free 0.238
7OXI ttSlyD with W4A pseudo-wild-type S2 peptide Deposited 2021-06-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 6.5；292.15 K；sodium cacodylate, MPD, PEG8000	Resolution 2.60 Å R-free 0.245
7OXJ ttSlyD with M8A pseudo-wild-type S2 peptide Deposited 2021-06-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	NI NICKEL (II) ION × 1 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；292.15 K；Sodium cacodylate, PEG 200	Resolution 1.85 Å R-free 0.224
7OXK ttSlyD with W4K pseudo-wild-type S2 peptide Deposited 2021-06-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 9；292.15 K；1-4dioxane, bicine, PEG 20000	Resolution 2.80 Å R-free 0.235

15 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5SLE7_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149 Author chain C； PDBConstruct 1–149； UniProt 1–149

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	4odo
Deposition date deposition_date	2014-01-10
Structure title title	Structure of SlyD from Thermus thermophilus in complex with FK506
Keywords keywords	FKBP domain, IF domain, chaperone, peptidyl-prolyl isomerase, PPIase, ISOMERASE; ISOMERASE, CHAPERONE
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	28.08 Å
Radius of gyration Rg (electron density) rg_electron	27.43 Å
Forward intensity I(0) i0	46177200.00
Molecular weight molecular_weight	52873.0 kDa
Excluded volume excluded_volume	66068 Å³
Envelope volume envelope_volume	86006 Å³
Hydration-shell volume shell_volume	27694 Å³
Envelope diameter envelope_diameter	98.9 Å
Shell Rg shell_rg	33.11 Å
Envelope Rg envelope_rg	26.83 Å
Shape Rg shape_rg	27.39 Å
Total Rg total_rg	28.15 Å
Total atoms total_atoms	3729
Residues n_residues	458
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	95.4 Å
Rg (real space) rg_real	28.24 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	4.6180e+07
I(0) uncertainty (real space) i0_real_error	7.1840e+05
Rg (reciprocal space) rg_reciprocal	28.19 Å
I(0) (reciprocal space) i0_reciprocal	46180000.0000
Solution quality estimate total_estimate	0.8676
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	0.491
Kurtosis Kurtosis kurtosis	-0.174
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7124000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.965

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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	Peptidyl-prolyl cis-trans isomerase SlyD
Molecular weight formula_weight	17400.2 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4385

MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH

来源 Source

来源生物 organism	Thermus thermophilus
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
Molecular weight formula_weight	804.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	629

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4odoA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4odoB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4odoC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	48.710 Å
Unit-cell length b length_b	50.210 Å
Unit-cell length c length_c	57.670 Å
Unit-cell angle α angle_alpha	85.74 °
Unit-cell angle β angle_beta	68.92 °
Unit-cell angle γ angle_gamma	80.12 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	1.599 Å
Low-resolution limit resolution_low	27.810 Å
R factor r_factor	0.1808
R_work r_work	0.1800
R_free r_free	0.2041

fit	/app/data/saxs_computation/od/4odo/4odo.fit
pddf	/app/data/pr_computation/od/4odo/4odo.pr.out
profile	/app/data/saxs_computation/od/4odo/4odo.dat

Structure of SlyD from Thermus thermophilus in complex with FK506