SAXSdb — 4kfz

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

LMO-2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 9–158	Fragment：UNP residues 9-158	Anti-LMO2 VH × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 9–158	Fragment：UNP residues 9-158	Anti-LMO2 VH × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258
3	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 9–158	Fragment：UNP residues 9-158	Anti-LMO2 VH × 6 ZN ZINC ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258
4	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain B； UniProt 9–158	Fragment：UNP residues 9-158	Anti-LMO2 VH × 6 ZN ZINC ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258

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 4KFZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XJY Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form Deposited 2010-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；25% PEG 1500 AND 100 MM SPG, BUFFER PH 4.0	Resolution 2.40 Å R-free 0.229
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2YPA Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA Deposited 2012-10-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 25–156（132 aa） Fragment：LIM, RESIDUES 25-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.80 Å R-free 0.269

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

View Construct and Data Evidence

UniProt name	RBTN2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 9–158 Author chain B； PDBConstruct 1–150； UniProt 9–158

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	4kfz
Deposition date deposition_date	2013-04-28
Structure title title	Crystal structure of LMO2 and anti-LMO2 VH complex
Keywords keywords	ONCOPROTEIN, T-CELL LEUKEMIA, PROTO-ONCOGENE, TRANSCRIPTION, DEVELOPMENTAL PROTEIN, LIM domain, transcription factor, nucleus; TRANSCRIPTION
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	31.23 Å
Radius of gyration Rg (electron density) rg_electron	31.23 Å
Forward intensity I(0) i0	69019700.00
Molecular weight molecular_weight	62532.0 kDa
Excluded volume excluded_volume	77029 Å³
Envelope volume envelope_volume	112410 Å³
Hydration-shell volume shell_volume	31419 Å³
Envelope diameter envelope_diameter	142.5 Å
Shell Rg shell_rg	35.58 Å
Envelope Rg envelope_rg	33.90 Å
Shape Rg shape_rg	31.30 Å
Total Rg total_rg	31.41 Å
Total atoms total_atoms	4350
Residues n_residues	548
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	81.2 Å
Rg (real space) rg_real	28.76 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	6.5310e+07
I(0) uncertainty (real space) i0_real_error	8.0560e+05
Rg (reciprocal space) rg_reciprocal	31.48 Å
I(0) (reciprocal space) i0_reciprocal	69010000.0000
Solution quality estimate total_estimate	0.6887
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.268
Kurtosis Kurtosis kurtosis	-0.507
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	1.4980
Highest regularization parameter α highest_alpha	4286000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.002; Oscil: 0.999; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	LMO-2
Molecular weight formula_weight	17479.3 kDa
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	4350

SLDPSEEPVDEVLQIPPSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKINGMI

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

Entity 2 Entity 2 polymer

Description description	Anti-LMO2 VH
Molecular weight formula_weight	14069.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GGSMAEVQLLESGGGLVQPGGSLRLSCAASGFSFSHSPMNWVRQAPGKGLEWVSYISYNSSSIYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGLTESLELTADWFDYWGQGTLVTVSS

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

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4kfzc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4kfzd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	4kfzA01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

Domain ID domain_id	4kfzA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

Domain ID domain_id	4kfzB01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

Domain ID domain_id	4kfzB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

Domain ID domain_id	4kfzC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kfzD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	124.260 Å
Unit-cell length b length_b	124.260 Å
Unit-cell length c length_c	81.440 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	12

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2399
R_work r_work	0.2390
R_free r_free	0.2583

fit	/app/data/saxs_computation/kf/4kfz/4kfz.fit
pddf	/app/data/pr_computation/kf/4kfz/4kfz.pr.out
profile	/app/data/saxs_computation/kf/4kfz/4kfz.dat

Crystal structure of LMO2 and anti-LMO2 VH complex

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

LMO-2

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)