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- PDB-3eyc: New crystal structure of human tear lipocalin in complex with 1,4... -

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Basic information

Entry
Database: PDB / ID: 3eyc
TitleNew crystal structure of human tear lipocalin in complex with 1,4-butanediol in space group P21
ComponentsLipocalin-1
KeywordsTRANSPORT PROTEIN / ligand-binding protein / beta-barrel / Secreted / Sensory transduction / Taste / Transport
Function / homology
Function and homology information


Transport of fatty acids / response to stimulus / chloride ion binding / cysteine-type endopeptidase inhibitor activity / small molecule binding / sensory perception of taste / signaling receptor binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
von Ebner's gland protein/ Bos/Can allergen / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / Lipocalin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBreustedt, D.A. / Keil, L. / Skerra, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity
Authors: Breustedt, D.A. / Chatwell, L. / Skerra, A.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipocalin-1
B: Lipocalin-1
C: Lipocalin-1
D: Lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1578
Polymers71,7974
Non-polymers3604
Water3,333185
1
A: Lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0392
Polymers17,9491
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0392
Polymers17,9491
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0392
Polymers17,9491
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0392
Polymers17,9491
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.907, 34.166, 143.481
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lipocalin-1 / / Von Ebner gland protein / VEG protein / Tear prealbumin / TP / Tear lipocalin / Tlc


Mass: 17949.180 Da / Num. of mol.: 4 / Fragment: residues 5-166 / Mutation: C101S, D158A
Source method: isolated from a genetically manipulated source
Details: Tear / Source: (gene. exp.) Homo sapiens (human) / Gene: LCN1 / Plasmid: pTlc3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P31025
#2: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.62 % / Mosaicity: 0.466 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 27% PEG3350, 0.8% 1.4-Butanediol, 200mM NaCl, 100mM Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: Osmics mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 19625 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.061 / Χ2: 1.037 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.69 Å / % possible obs: 97 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.236 / Num. unique obs: 1852 / Χ2: 0.991

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xki, residues 14 to 24, 38 to 55, 64 to 104 and 110 to 150

1xki


Resolution: 2.6→20 Å / FOM work R set: 0.798 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 1000 Random
Rwork0.228 --
obs-19581 -
Displacement parametersBiso mean: 43.683 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 24 185 4524
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.299
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.6-2.640.244400.296888928
2.64-2.690.57410.354895936
2.69-2.740.45590.319900959
2.74-2.80.443490.335927976
2.8-2.860.406480.307935983
2.86-2.930.314650.296895960
2.93-30.278340.288925959
3-3.080.407490.277946995
3.08-3.170.219510.231904955
3.17-3.270.307590.256918977
3.27-3.390.281470.244936983
3.39-3.520.244480.222920968
3.52-3.680.301460.242938984
3.68-3.880.209540.2936990
3.88-4.120.23530.184912965
4.12-4.430.28440.1999571001
4.43-4.870.242530.1769581011
4.87-5.570.212490.194942991
5.57-6.960.261490.2179641013
6.96-200.238620.2129851047

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