SAXSdb — 6fl5

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

Serine hydroxymethyltransferase, cytosolic

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 11–481 Chain D； UniProt 11–481 Chain G； UniProt 11–481 Chain J； UniProt 11–481	Mutation：H135N, R137A, E168N	PLP PYRIDOXAL-5'-PHOSPHATE × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；2 microL of 80microM protein solution in: 20 mM Hepes pH7.2, 250 mM NaCl 5% glycerol + 2 microL of reservoir:0.1 M Na Cacodilate pH6.5 - 1M Na citrate	Resolution 3.60 Å R-free 0.277

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 6FL5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJ4 RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (HUMAN) Deposited 1998-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–480（470 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；2 M SODIUM ACETATE, PH 6.5	Resolution 2.65 Å R-free 0.226
6M5W Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid Deposited 2020-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 4 DXC (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID × 4 GLY GLYCINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, and 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH)	Resolution 3.10 Å R-free 0.233
7RJL Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT Deposited 2021-07-21	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 C 270–275（6 aa） Fragment：UNP residues 270-275	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；35% v/v Tacsimate	Resolution 1.50 Å R-free 0.185
7RJL Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT Deposited 2021-07-21	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 D 270–275（6 aa） Fragment：UNP residues 270-275	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；35% v/v Tacsimate	Resolution 1.50 Å R-free 0.185
7RJP Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT Deposited 2021-07-21	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 B 270–275（6 aa） Fragment：UNP residues 270-275	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 8 CL CHLORIDE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris	Resolution 1.25 Å R-free 0.174
8A11 Cryo-EM structure of the Human SHMT1-RNA complex Deposited 2022-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa） Chain B 1–483（483 aa） Chain C 1–483（483 aa） Chain D 1–483（483 aa）	Mutation：Chain B has not PLP bond to the active site Mutation：Chain B has not PLP bond to the active site Mutation：Chain B has not PLP bond to the active site Mutation：Chain B has not PLP bond to the active site	PLP PYRIDOXAL-5'-PHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 4 seconds before plunging	Resolution 3.52 Å
8R7H Cryo-EM structure of Human SHMT1 Deposited 2023-11-24	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa） Chain B 1–483（483 aa） Chain C 1–483（483 aa） Chain D 1–483（483 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 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 4 seconds before plunging	Resolution 3.29 Å
8XND Crystal structure of serine hydroxymethyltransferase 1 Deposited 2023-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 11–480（470 aa） Chain D 11–480（470 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES pH 7.5,30 %(v/v) PEG 300	Resolution 3.45 Å R-free 0.192
8XND Crystal structure of serine hydroxymethyltransferase 1 Deposited 2023-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 11–480（470 aa） Chain C 11–480（470 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES pH 7.5,30 %(v/v) PEG 300	Resolution 3.45 Å R-free 0.192

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLYC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 11–481 Author chain D； PDBConstruct 1–471； UniProt 11–481 Author chain G； PDBConstruct 1–471； UniProt 11–481 Author chain J； PDBConstruct 1–471； UniProt 11–481

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	6fl5
Deposition date deposition_date	2018-01-25
Structure title title	Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution
Keywords keywords	Transferase, serine hydroxymethyltransferase, Interface, Tetramer, OCM, serine, THF, glicine, TCA; TRANSFERASE
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	39.58 Å
Radius of gyration Rg (electron density) rg_electron	39.03 Å
Forward intensity I(0) i0	632824000.00
Molecular weight molecular_weight	204740.0 kDa
Excluded volume excluded_volume	255780 Å³
Envelope volume envelope_volume	324200 Å³
Hydration-shell volume shell_volume	67305 Å³
Envelope diameter envelope_diameter	124.7 Å
Shell Rg shell_rg	46.22 Å
Envelope Rg envelope_rg	38.50 Å
Shape Rg shape_rg	39.02 Å
Total Rg total_rg	39.42 Å
Total atoms total_atoms	14389
Residues n_residues	1866
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	122.5 Å
Rg (real space) rg_real	39.44 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	6.3280e+08
I(0) uncertainty (real space) i0_real_error	1.1280e+07
Rg (reciprocal space) rg_reciprocal	39.53 Å
I(0) (reciprocal space) i0_reciprocal	632900000.0000
Solution quality estimate total_estimate	0.9008
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.9 Å
Skewness Skewness skewness	0.196
Kurtosis Kurtosis kurtosis	-0.647
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	149200000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.827

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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	Serine hydroxymethyltransferase, cytosolic
Molecular weight formula_weight	51695.8 kDa
EC 编号 ec_number	2.1.2.1
Mutation mutation	H135N, R137A, E168N
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	14389

DADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQPYSGSPANFAVYTALVEPNGAIMGLDLPDGGHLTHGFMTDKKKISATSIFFNSMPYKVNPDTGYINYDQLEENARLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVAAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAAVQALREEVESFASLFPLPGLP

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 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	4

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6fl5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	6fl5D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	6fl5G01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	6fl5J01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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8. Citations (1)

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Unit-cell length a length_a	139.719 Å
Unit-cell length b length_b	139.719 Å
Unit-cell length c length_c	267.377 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	50.010 Å
R factor r_factor	0.2630
R_work r_work	0.2622
R_free r_free	0.2771

fit	/app/data/saxs_computation/fl/6fl5/6fl5.fit
pddf	/app/data/pr_computation/fl/6fl5/6fl5.pr.out
profile	/app/data/saxs_computation/fl/6fl5/6fl5.dat

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

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

Serine hydroxymethyltransferase, cytosolic

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