SAXSdb — 4q7l

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

Uncharacterized ABC transporter ATP-binding protein TM_0288

Thermotoga maritima

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 353–598	Fragment：unp residues 353-598	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.35 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 353–598	Fragment：unp residues 353-598	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.35 Å R-free 0.236
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 353–598	Fragment：unp residues 353-598	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.35 Å R-free 0.236

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 4Q7L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QF4 Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation Deposited 2011-01-21	Different construct 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 1–598（598 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.90 Å R-free 0.263
4Q4A Improved model of AMP-PNP bound TM287/288 Deposited 2014-04-14	Different construct 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 1–598（598 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293.15 K；29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, temperature 293.15K	Resolution 2.60 Å R-free 0.268
4Q4H TM287/288 in its apo state Deposited 2014-04-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–598（598 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；26 % (w/v) polyethylene glycol (PEG) 400, 50 mM Na-cacodylate, 50 mM CaCl2, 2.5 mM ADP and 3 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.53 Å R-free 0.290
4Q4J Structure of crosslinked TM287/288_S498C_S520C mutant Deposited 2014-04-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–598（598 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；32 % PEG 400, 50 mM Na-Acetate pH 5 and 500 mM KCl, 2.5 mM AMP-PNP, 3 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.20 Å R-free 0.287
4Q7M Structure of NBD288-Avi of TM287/288 Deposited 2014-04-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 353–598（246 aa） Fragment：unp residues 353-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；100 mM Sodium acetate, 6 % PEG550 MME, 6 % PEG20000, 200 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.30 Å R-free 0.236
6QUZ Structure of ATPgS-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different construct Different mutation/modification 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 1–598（598 aa） Fragment：ABC transporter	Mutation：E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.035M NaCl, 11.5% (w/v) PEG 6000	Resolution 3.21 Å R-free 0.263
6QUZ Structure of ATPgS-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.035M NaCl, 11.5% (w/v) PEG 6000	Resolution 3.21 Å R-free 0.263
6QV0 Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different construct Different mutation/modification 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 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000	Resolution 3.12 Å R-free 0.264
6QV0 Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000	Resolution 3.12 Å R-free 0.264
6QV1 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM1 Deposited 2019-03-01	Different construct Different mutation/modification 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 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME	Resolution 3.48 Å R-free 0.303
6QV1 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM1 Deposited 2019-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME	Resolution 3.48 Å R-free 0.303
6QV2 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 Deposited 2019-03-01	Different construct Different mutation/modification 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 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400	Resolution 4.23 Å R-free 0.330
6QV2 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 Deposited 2019-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400	Resolution 4.23 Å R-free 0.330

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Y288_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–248； UniProt 353–598 Author chain B； PDBConstruct 3–248； UniProt 353–598 Author chain C； PDBConstruct 3–248； UniProt 353–598

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	4q7l
Deposition date deposition_date	2014-04-25
Structure title title	Structure of NBD288 of TM287/288
Keywords keywords	ABC-tpye Nucleotide Binding Domain (NBD), METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	36.92 Å
Radius of gyration Rg (electron density) rg_electron	36.51 Å
Forward intensity I(0) i0	100715000.00
Molecular weight molecular_weight	83699.0 kDa
Excluded volume excluded_volume	106360 Å³
Envelope volume envelope_volume	150110 Å³
Hydration-shell volume shell_volume	35101 Å³
Envelope diameter envelope_diameter	131.9 Å
Shell Rg shell_rg	41.73 Å
Envelope Rg envelope_rg	35.55 Å
Shape Rg shape_rg	36.53 Å
Total Rg total_rg	36.83 Å
Total atoms total_atoms	5899
Residues n_residues	742
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	123.7 Å
Rg (real space) rg_real	36.96 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	1.0070e+08
I(0) uncertainty (real space) i0_real_error	1.9880e+06
Rg (reciprocal space) rg_reciprocal	36.94 Å
I(0) (reciprocal space) i0_reciprocal	100700000.0000
Solution quality estimate total_estimate	0.6553
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.9 Å
Skewness Skewness skewness	0.279
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7030000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.940; Smooth: 0.771

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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	Uncharacterized ABC transporter ATP-binding protein TM_0288
Molecular weight formula_weight	28878.3 kDa
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	6168

MSGEIEFKNVWFSYDKKKPVLKDITFHIKPGQKVALVGPTGSGKTTIVNLLMRFYDVDRGQILVDGIDIRKIKRSSLRSSIGIVLQDTILFSTTVKENLKYGNPGATDEEIKEAAKLTHSDHFIKHLPEGYETVLTDNGEDLSQGQRQLLAITRAFLANPKILILDEATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNTIKNADLIIVLRDGEIVEMGKHDELIQKRGFYYELFTSQYGLVVEKEAALEVLFQ

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	218

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4q7la1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d4q7la2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4q7la3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4q7lb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d4q7lb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4q7lb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4q7lc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d4q7lc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	4q7lA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4q7lB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4q7lC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	95.930 Å
Unit-cell length b length_b	95.930 Å
Unit-cell length c length_c	88.510 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	9

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	47.965 Å
R factor r_factor	0.1952
R_work r_work	0.1931
R_free r_free	0.2363

fit	/app/data/saxs_computation/q7/4q7l/4q7l.fit
pddf	/app/data/pr_computation/q7/4q7l/4q7l.pr.out
profile	/app/data/saxs_computation/q7/4q7l/4q7l.dat

Structure of NBD288 of TM287/288

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

Uncharacterized ABC transporter ATP-binding protein TM_0288

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