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- PDB-3t1d: The mutant structure of human Siderocalin W79A, R81A, Y106F bound... -

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Basic information

Entry
Database: PDB / ID: 3t1d
TitleThe mutant structure of human Siderocalin W79A, R81A, Y106F bound to Enterobactin
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsANTIMICROBIAL PROTEIN / SSGCID / Seattle Structural Genomics Center for Infectious Disease / beta-barrel / siderocalin / W79A / R81A / Y106F
Function / homology
Function and homology information


Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-BENZOIC ACID / Chem-DBS / Chem-TD1 / Gene 8 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct phasing from previous structure / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J Struct Biol X / Year: 2019
Title: Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands.
Authors: Clifton, M.C. / Rupert, P.B. / Hoette, T.M. / Raymond, K.N. / Abergel, R.J. / Strong, R.K.
History
DepositionJul 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.5Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 1.6Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,85818
Polymers67,1423
Non-polymers1,71615
Water4,666259
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,18410
Polymers22,3811
Non-polymers8039
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9605
Polymers22,3811
Non-polymers5804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7143
Polymers22,3811
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.749, 114.749, 119.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / p25


Mass: 22380.715 Da / Num. of mol.: 3 / Mutation: W79A, R81A, Y106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P80188

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Non-polymers , 7 types, 274 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TD1 / O-[(2S)-2-amino-3-hydroxypropanoyl]-N-(2,3-dihydroxybenzoyl)-L-serine


Mass: 328.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O8
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Chemical ChemComp-DBS / 2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID / 2,3,-DIHYDROXYBENZOYLSERINE


Type: L-peptide linking / Mass: 241.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO6
#7: Chemical ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE AUTHORS STATE C87S IS A MUTATION IN ALL SIDEROCALIN STRUCTURES

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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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate. Protein 10 mg/ml, Cryoprotection 15% glycerol. Target DB: HosaA.18070.a, pH 4.5, VAPOR DIFFUSION, ...Details: 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate. Protein 10 mg/ml, Cryoprotection 15% glycerol. Target DB: HosaA.18070.a, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34877 / % possible obs: 96.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Χ2: 1.003 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.344.80.52417500.977199.1
2.34-2.385.10.45917330.977199
2.38-2.435.50.42217420.947198.6
2.43-2.485.80.38517301.001198.5
2.48-2.535.80.34217491.011198.4
2.53-2.595.90.31217401.014198.4
2.59-2.665.80.27617361198.1
2.66-2.735.90.23317411.008197.6
2.73-2.815.90.18717371.002197.7
2.81-2.95.90.16617411.035198.1
2.9-35.90.12217441.057197.5
3-3.125.90.09417391.036197
3.12-3.265.90.07817321.067197.1
3.26-3.445.90.06217431.045197
3.44-3.655.90.04717291.001196.4
3.65-3.935.90.04117451.048195.6
3.93-4.335.90.03217230.912195.5
4.33-4.955.90.02617451.059194.5
4.95-6.245.90.0317550.984193.9
6.24-505.60.02518230.866191.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: Direct phasing from previous structure
Starting model: 1L6M

1l6m


Resolution: 2.3→48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2278 / WRfactor Rwork: 0.1885 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8598 / SU B: 9.893 / SU ML: 0.126 / SU R Cruickshank DPI: 0.2663 / SU Rfree: 0.2087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 3323 9.6 %RANDOM
Rwork0.1885 ---
obs0.1923 34690 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.92 Å2 / Biso mean: 32.1301 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 114 259 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024391
X-RAY DIFFRACTIONr_bond_other_d0.0010.022970
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9825966
X-RAY DIFFRACTIONr_angle_other_deg0.8743.0027267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28724.874199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30415709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.161515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02884
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 232 -
Rwork0.249 2134 -
all-2366 -
obs--98.62 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0941-1.2328-0.08981.57320.27892.3377-0.0498-0.02630.0071-0.0556-0.021-0.05590.13250.07810.07080.06940.00180.02960.01160.02130.069249.172249.903644.8719
20.52050.21240.55632.7150.76733.5841-0.06060.1328-0.2754-0.18350.0082-0.0980.2560.13530.05240.086-0.0390.0530.0936-0.04770.201241.570140.630337.2333
31.5818-0.11040.06451.0502-0.68781.69380.01380.0174-0.0606-0.0918-0.02650.00770.13110.02180.01270.0399-0.01280.00090.0262-0.010.034647.47747.459945.563
44.98381.95192.88742.48120.96073.1147-0.13330.3950.2948-0.2287-0.12090.02420.03130.15920.25410.08810.01560.03820.08210.0350.04352.02549.434233.8845
55.3075-0.6689-0.52712.3144-0.07191.6358-0.1292-0.0874-0.0620.11020.14660.00070.07970.0548-0.01740.07950.0475-0.00770.0477-0.02380.025376.204428.137265.2454
61.5238-1.3667-0.07592.0265-1.05183.04510.04270.2530.0947-0.06790.0087-0.06730.01080.0234-0.05140.05540.0081-0.00370.20460.00340.10969.607434.6254.2463
72.466-0.5517-0.20372.0218-0.00370.905-0.06480.0479-0.06320.0360.0902-0.0310.06960.0479-0.02540.05610.04580.0010.04940.00530.023774.92626.852462.3688
85.1128-2.78272.07222.8615-0.75122.4877-0.2391-0.20040.56270.21380.1996-0.2784-0.1388-0.03250.03950.03910.0167-0.00150.0569-0.03940.106279.653438.385263.6813
95.3981.6559-6.24792.9799-0.689311.9490.198-0.61770.45850.21670.00390.2165-0.44050.664-0.20190.13940.05830.00470.1586-0.04390.065480.13152.714573.5286
103.27451.18370.67782.39171.19951.4789-0.20410.2855-0.1566-0.38460.09480.05190.0871-0.28980.10930.2629-0.06840.0070.1895-0.05450.023371.5915-5.539357.5365
114.9093-1.9305-2.37024.46011.55033.9155-0.0159-0.13070.1415-0.07310.01970.144-0.03420.0093-0.00370.0993-0.0029-0.01590.02680.00070.018273.73934.277363.9017
123.02560.68880.33092.16880.89223.6447-0.0562-0.1348-0.62540.05320.1138-0.17390.55030.2711-0.05760.17980.09620.01930.0620.030.130278.2834-11.174567.0153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 42
2X-RAY DIFFRACTION2A43 - 79
3X-RAY DIFFRACTION3A80 - 153
4X-RAY DIFFRACTION4A154 - 177
5X-RAY DIFFRACTION5B5 - 43
6X-RAY DIFFRACTION6B44 - 79
7X-RAY DIFFRACTION7B80 - 153
8X-RAY DIFFRACTION8B154 - 178
9X-RAY DIFFRACTION9C5 - 20
10X-RAY DIFFRACTION10C21 - 81
11X-RAY DIFFRACTION11C82 - 131
12X-RAY DIFFRACTION12C132 - 177

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