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- PDB-9xxu: Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of... -

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Basic information

Entry
Database: PDB / ID: 9xxu
TitleCrystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution
Components
  • C-terminal fragment of Lactotransferrin
  • Lactotransferrin
KeywordsMETAL BINDING PROTEIN / C-LOBE / LACTOFERRIN / IRON BINDING / CLF
Function / homology
Function and homology information


Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / iron ion transport / recycling endosome / antibacterial humoral response / early endosome / iron ion binding / signaling receptor binding / serine-type endopeptidase activity / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
ACETATE ION / Lactotransferrin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsPandit, S. / Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution
Authors: Pandit, S. / Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactotransferrin
C: C-terminal fragment of Lactotransferrin
B: Lactotransferrin
D: C-terminal fragment of Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,79918
Polymers75,7344
Non-polymers5,06614
Water73941
1
A: Lactotransferrin
C: C-terminal fragment of Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,53911
Polymers37,8672
Non-polymers2,6729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint17 kcal/mol
Surface area16790 Å2
MethodPISA
2
B: Lactotransferrin
D: C-terminal fragment of Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2607
Polymers37,8672
Non-polymers2,3935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-3 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.684, 139.060, 120.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-805-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Lactotransferrin / Lactoferrin


Mass: 36842.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: the protein got cleaved after Leu680 thereby generating two protein frqgments
Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide C-terminal fragment of Lactotransferrin / Lactoferrin


Mass: 1024.214 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Sugars , 3 types, 6 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 49 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate trihydrate (pH 4.6), 0.2M ammonium sulfate, 25% w/v PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.82→47.583 Å / Num. obs: 19057 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 72.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.096 / Net I/σ(I): 8.3
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 7 % / Rmerge(I) obs: 1.497 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2752 / CC1/2: 0.535 / Rpim(I) all: 0.912 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MxCuBEdata collection
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→47.583 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.193 / Average fsc free: 0.937 / Average fsc work: 0.9544 / Cross valid method: FREE R-VALUE / ESU R Free: 0.417
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2686 371 1.948 %
Rwork0.2114 18675 -
all0.213 --
obs-19046 99.343 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 79.726 Å2
Baniso -1Baniso -2Baniso -3
1-3.317 Å2-0 Å20 Å2
2---3.681 Å20 Å2
3---0.363 Å2
Refinement stepCycle: LAST / Resolution: 2.82→47.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 333 41 5556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125654
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165189
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.8357708
X-RAY DIFFRACTIONr_angle_other_deg1.8971.76512046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6175680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.706525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7910893
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.38610231
X-RAY DIFFRACTIONr_chiral_restr0.1350.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026409
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021195
X-RAY DIFFRACTIONr_nbd_refined0.2360.21387
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.25141
X-RAY DIFFRACTIONr_nbtor_refined0.180.22848
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1020.22871
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.229
X-RAY DIFFRACTIONr_nbd_other0.1860.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.214
X-RAY DIFFRACTIONr_mcbond_it5.0657.582727
X-RAY DIFFRACTIONr_mcbond_other5.0657.582727
X-RAY DIFFRACTIONr_mcangle_it8.07813.6123401
X-RAY DIFFRACTIONr_mcangle_other8.07713.6143402
X-RAY DIFFRACTIONr_scbond_it5.7778.7622927
X-RAY DIFFRACTIONr_scbond_other5.7668.7662916
X-RAY DIFFRACTIONr_scangle_it9.4715.9134306
X-RAY DIFFRACTIONr_scangle_other9.46115.9214289
X-RAY DIFFRACTIONr_lrange_it15.33395.58523601
X-RAY DIFFRACTIONr_lrange_other15.33495.59523592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.82-2.8930.336240.39813640.39713920.9070.88599.71260.392
2.893-2.9720.435220.37513330.37613580.870.89699.77910.368
2.972-3.0580.39280.32512700.32613030.8920.92299.61630.313
3.058-3.1520.351230.28412570.28612830.8970.94199.76620.263
3.152-3.2540.328190.27112340.27112580.9410.94799.60250.248
3.254-3.3680.432240.25311640.25711940.8860.95799.49750.233
3.368-3.4950.222130.23711830.23711960.9680.9641000.219
3.495-3.6360.265230.21410860.21511110.9620.97399.820.197
3.636-3.7970.204220.19310590.19310830.9740.97799.81530.176
3.797-3.9810.205190.18810300.18810500.9660.97799.90480.172
3.981-4.1950.269210.1959620.1979860.9540.97499.69570.179
4.195-4.4470.34170.1919040.1949240.9230.97599.67530.179
4.447-4.7510.304200.178520.1738770.9480.9899.42990.16
4.751-5.1280.139150.1838020.1828300.990.98198.43370.176
5.128-5.6110.314230.1877320.197640.9470.9898.8220.177
5.611-6.2620.279180.1846700.1866910.9510.97999.56580.176
6.262-7.210.30790.1536110.1546260.960.98499.04150.149
7.21-8.780.18130.1595160.165390.9750.98398.14470.16
8.78-12.2110.222130.1714060.1734340.9740.98296.54380.177
12.211-47.5830.26750.2632400.2632680.9980.94191.41790.317

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