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3cr9

Crystal structure of the complex of Lactoferrin with 6-(Hydroxymethyl)oxane-2,3,4,5-tetrol at 3.49 A resolution

Method: X-RAY DIFFRACTION Dmax: 97.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lactotransferrin

OrganismNot specified

UniProt O77811

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 7–695 Not recorded GLC alpha-D-glucopyranose × 1 FE FE (III) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；50mM Tris, pH 8, 21% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.49 Å R-free 0.226

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 3CR9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B1X STRUCTURE OF DIFERRIC MARE LACTOFERRIN AT 2.62A RESOLUTION Deposited 1998-11-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–695（689 aa）
Not recorded FE FE (III) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；40MG/ML PROTEIN IN 10MM TRIS HCL, PH 8.5, MICRODIALYSED AGA AT 6 DEGREES CELSIUS
Resolution 2.62 Å R-free 0.264
1B7U Structure of Mare Apolactoferrin: the N and C Lobes are in the Closed Form Deposited 1999-01-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–695（689 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；pH 8.5, VAPOR DIFFUSION, HANGING DROP
Resolution 3.80 Å R-free 0.300
1B7Z STRUCTURE OF OXALATE SUBSTITUTED DIFERRIC MARE LACTOFERRIN FROM COLOSTRUM Deposited 1999-01-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–695（689 aa）
Not recorded FE FE (III) ION × 2 OXL OXALATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30 MG/ML PROTEIN IN 0.025M TRIS-HCL DIALYZED AGAINST SAME BUFFER MADE AS 10% (V/V) ETHANOL AT PH 8.5
Resolution 2.70 Å R-free 0.274
1F9B MELANIN PROTEIN INTERACTION: X-RAY STRUCTURE OF THE COMPLEX OF MARE LACTOFERRIN WITH MELANIN MONOMERS Deposited 2000-07-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–695（695 aa）
Not recorded FE FE (III) ION × 2 BCT BICARBONATE ION × 2 3ID 3H-INDOLE-5,6-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 5；277 K；20mM Tris-Hcl, pH 5.0 concentration 50 mg/ml 10% ethanol soaked for 12hours in buffer containing DOPA, MICRODIALYSIS, temperature 4K
Resolution 2.70 Å R-free 0.287
1I6B STRUCTURE OF EQUINE APOLACTOFERRIN AT 3.2 A RESOLUTION USING CRYSTALS GROWN AT 303K Deposited 2001-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–695（689 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 8；303 K；ethanol, pH 8.0, MICRODIALYSIS, temperature 303K
Resolution 3.20 Å R-free 0.291
1QJM Crystal Structure of a Complex of Lactoferrin with a Lanthanide Ion (SM3+) at 3.4 Angstrom Resolution Deposited 1999-06-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–695（689 aa）
Not recorded SM SAMARIUM (III) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；277 K；PROTEIN SOLUTION WITH A CONCENTRATION OF 40MG/ML IN 0.025M TRIS-HCL WAS EQUILIBRATED AGAINST THE SAME BUFFER CONTAINING 10% (V/V) ETHANOL AT PH 8.0 AT 4 DEGREE.
Resolution 3.40 Å R-free 0.316

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRFL_HORSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–689； UniProt 7–695

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3cr9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cr9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cr9
Deposition date deposition_date2008-04-05
Structure title titleCrystal structure of the complex of Lactoferrin with 6-(Hydroxymethyl)oxane-2,3,4,5-tetrol at 3.49 A resolution
Keywords keywords;IRON BINDING PROTEIN, LACTOFERRIN, ANTIBACTERIAL, 6-(HYDROXYMETHYL)OXANE-2, 3, 4, 5-tetrol, Glycoprotein, Hydrolase, Metal Binding Protein, Ion transport, Iron, Iron transport, Metal-binding, Protease, Secreted, Serine protease, Transport, ANTIBIOTIC ;; ANTIBIOTIC
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.29 Å
Radius of gyration Rg (electron density) rg_electron29.48 Å
Forward intensity I(0) i098359000.00
Molecular weight molecular_weight75576.0 kDa
Excluded volume excluded_volume93524 ų
Envelope volume envelope_volume117220 ų
Hydration-shell volume shell_volume33512 ų
Envelope diameter envelope_diameter100.5 Å
Shell Rg shell_rg36.30 Å
Envelope Rg envelope_rg29.23 Å
Shape Rg shape_rg29.46 Å
Total Rg total_rg30.15 Å
Total atoms total_atoms5295
Residues n_residues689
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax97.0 Å
Rg (real space) rg_real30.32 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real9.8360e+07
I(0) uncertainty (real space) i0_real_error1.5960e+06
Rg (reciprocal space) rg_reciprocal30.31 Å
I(0) (reciprocal space) i0_reciprocal98360000.0000
Solution quality estimate total_estimate0.8933
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.9 Å
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.623
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24080000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cr9a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.2 — Transferrin
Domain ID domain_idd3cr9a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.2 — Transferrin

CATH v4.4 (4 domains)

Domain ID domain_id3cr9A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id3cr9A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id3cr9A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id3cr9A04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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8. Citations (1)

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9. Files and Curves (10)