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- PDB-2xst: Crystal Structure of the Human Lipocalin 15 -

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Basic information

Entry
Database: PDB / ID: 2xst
TitleCrystal Structure of the Human Lipocalin 15
ComponentsLIPOCALIN 15
KeywordsTRANSPORT PROTEIN / LCN15 / MSFL2541
Function / homology
Function and homology information


Transport of fatty acids / small molecule binding / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMuniz, J.R.C. / Gileadi, C. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Phillips, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Muniz, J.R.C. / Gileadi, C. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Phillips, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Human Lipocalin 15
Authors: Muniz, J.R.C. / Gileadi, C. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Phillips, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U.
History
DepositionSep 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Source and taxonomy ...Database references / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOCALIN 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0822
Polymers18,0191
Non-polymers621
Water2,594144
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.800, 44.800, 126.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein LIPOCALIN 15


Mass: 18019.486 Da / Num. of mol.: 1 / Fragment: LIPOCALIN 15 PRECURSOR, RESIDUES 19-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q6UWW0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.04 Å3/Da / Density % sol: 39.67 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH7.5, 1.4 M TRI-SODIUM CITRATE DIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→38.8 Å / Num. obs: 17872 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 21.98 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 1.6

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Processing

Software
NameVersionClassification
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→38.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.9563 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 912 5.11 %RANDOM
Rwork0.1561 ---
obs0.1576 17841 --
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.5594 Å20 Å20 Å2
2---2.5594 Å20 Å2
3---5.1189 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.63→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 4 144 1315
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011232HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.081673HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d564SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes181HARMONIC5
X-RAY DIFFRACTIONt_it1232HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion2.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion153SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1507SEMIHARMONIC4
LS refinement shellResolution: 1.63→1.73 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.241 168 5.86 %
Rwork0.2036 2700 -
all0.2059 2868 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.85810.0361-2.52567.6216-3.31171.7442-0.0687-0.2199-0.04990.1887-0.033-0.4229-0.23270.15190.1017-0.0351-0.0325-0.0764-0.1131-0.0236-0.122739.108311.249724.5411
21.0376-0.15571.04661.7061-1.2832.9119-0.099-0.026-0.02030.0190.19260.2926-0.1608-0.5044-0.0936-0.05910.0614-0.00590.04690.0152-0.050219.95457.242820.2866
35.75083.50572.0214.4233-1.32694.8892-0.14480.3877-0.237-0.11980.0087-0.24660.30820.18310.13610.04360.02530.0019-0.0064-0.0379-0.026335.6605-2.92520.1004
4-0.69741.0864-0.63041.487-1.6160.50850.0323-0.0188-0.11720.00660.00960.24180.0989-0.1695-0.04190.1602-0.0953-0.06470.24570.0170.086619.3334-4.956319.7701
50.95270.0074-0.48260.9286-0.44891.0421-0.03270.0585-0.1241-0.0810.0375-0.03950.1052-0.0179-0.0047-0.0215-0.0359-0.0107-0.02990.0072-0.103934.20584.874413.9045
61.5263-0.15090.32341.079-1.40052.8826-0.13940.10970.09690.08680.11050.1316-0.3787-0.18510.02890.02680.0383-0.0135-0.0337-0.0057-0.067826.782610.400620.633
71.522-0.78110.66233.3233-0.57236.0252-0.0432-0.21030.46480.28240.01740.2523-0.8273-0.41280.0259-0.01740.16150.0356-0.11340.0188-0.130120.731917.706623.9728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 22 A 32
2X-RAY DIFFRACTION2A 33 A 63
3X-RAY DIFFRACTION3A 64 A 75
4X-RAY DIFFRACTION4A 76 A 85
5X-RAY DIFFRACTION5A 86 A 110
6X-RAY DIFFRACTION6A 111 A 145
7X-RAY DIFFRACTION7A 146 A 172

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