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- PDB-4tnn: Crystal structure of Escherichia coli protein YodA in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4tnn
TitleCrystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.
ComponentsMetal-binding lipocalin
KeywordsMETAL BINDING PROTEIN / YodA / purification artifact / metal-binding lipocalin
Function / homologyCalycin beta-barrel core domain / Lipocalin / Beta Barrel / Mainly Beta / NICKEL (II) ION / :
Function and homology information
Biological speciesEscherichia coli str. K-12 substr. MC4100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsGasiorowska, O.A. / Cymborowski, M.T. / Handing, K.B. / Shabalin, I.G. / Zasadzinska, E. / Niedzialkowska, E. / Porebski, P.J. / Minor, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053163 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Protein purification and crystallization artifacts: The tale usually not told.
Authors: Niedzialkowska, E. / Gasiorowska, O. / Handing, K.B. / Majorek, K.A. / Porebski, P.J. / Shabalin, I.G. / Zasadzinska, E. / Cymborowski, M. / Minor, W.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Refinement description
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.6Sep 27, 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

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Assembly

Deposited unit
A: Metal-binding lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0098
Polymers22,3741
Non-polymers6357
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.583, 76.583, 61.944
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-204-

SO4

21A-353-

HOH

31A-362-

HOH

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Components

#1: Protein Metal-binding lipocalin


Mass: 22373.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MC4100 (bacteria)
Gene: yodA, BN896_1774 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: U6NCE6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 ul of 9.6 mg/ml protein in 50mM Tris pH 7.9, 300 mM NaCl and 0.5mM TCEP were mixed with 0.3 ul of the SaltRx condition #65 (2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0) and ...Details: 0.3 ul of 9.6 mg/ml protein in 50mM Tris pH 7.9, 300 mM NaCl and 0.5mM TCEP were mixed with 0.3 ul of the SaltRx condition #65 (2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0) and equilibrated against 1.5 M NaCl in MRC 2 drops 96 Well Crystallization Plate (Swissci)
PH range: 7.0-7.9 / Temp details: Rigaku Gallery 700

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 15647 / Num. obs: 15635 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Χ2: 1.245 / Net I/av σ(I): 30.528 / Net I/σ(I): 9 / Num. measured all: 114111
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.95-1.987.40.7672.417500.82100
1.98-2.027.40.627830.802100
2.02-2.067.40.5427740.853100
2.06-2.17.30.4527480.86899.9
2.1-2.157.40.3957820.896100
2.15-2.27.40.3237680.907100
2.2-2.257.40.2697820.978100
2.25-2.317.40.2387681.011100
2.31-2.387.40.2147751.021100
2.38-2.467.40.1927791.079100
2.46-2.547.40.1627721.135100
2.54-2.657.40.1417811.208100
2.65-2.777.30.1247611.238100
2.77-2.917.40.17801.346100
2.91-3.17.30.0847931.626100
3.1-3.337.30.0717851.831100
3.33-3.677.20.068022.13100
3.67-4.27.20.0467872.012100
4.2-5.297.20.0368141.474100
5.29-506.60.0398511.64599.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
MLPHAREphasing
DMphasing
Cootmodel building
PDB_EXTRACT3.14data extraction
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OEJ

1oej


Resolution: 1.951→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.694 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.146 / SU Rfree Cruickshank DPI: 0.1454 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 782 5 %RANDOM
Rwork0.1666 14834 --
obs0.1689 15616 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.69 Å2 / Biso mean: 36.632 Å2 / Biso min: 20.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å2-0 Å2
2--0.2 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.951→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 31 137 1714
Biso mean--54.9 41.03 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191620
X-RAY DIFFRACTIONr_bond_other_d0.0060.021406
X-RAY DIFFRACTIONr_angle_refined_deg1.51.952200
X-RAY DIFFRACTIONr_angle_other_deg0.77233255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2062582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.162154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_mcbond_it1.4161.902773
X-RAY DIFFRACTIONr_mcbond_other1.4171.903772
X-RAY DIFFRACTIONr_mcangle_it2.022.844965
LS refinement shellResolution: 1.951→2.002 Å
RfactorNum. reflection% reflection
Rfree0.212 67 5 %
Rwork0.207 1053 -
obs--100 %
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)
11.52550.90981.81131.48040.2823.50470.00230.1365-0.0627-0.03720.0659-0.15331.14920.8591-0.06820.08770.0466-0.02640.051-0.02120.045810.44941.2751.87
21.58820.1608-0.02643.1742-2.18333.14170.09540.1222-0.1470.0505-0.1854-0.2801-0.03510.4430.09010.0918-0.0296-0.0380.2045-0.0070.06896.4732.283-10.753
37.1096-4.33531.73863.7637-0.15731.1932-0.2051-1.0985-0.08250.35010.3196-0.06330.1346-0.457-0.11450.1699-0.06940.06410.50460.01830.0861-12.67135.1374.63
45.981-2.653-2.048716.9259-6.759210.38350.65920.06460.64610.0885-0.40250.0744-0.86320.4851-0.25670.1391-0.05780.11530.1614-0.01470.1928-18.95645.211-3.958
56.6422-4.11730.03384.89670.47532.31960.1529-0.2848-0.68910.366-0.00570.41920.2737-0.2056-0.14730.1226-0.0829-0.02260.17430.10310.1551-8.66621.8490.447
61.0769-0.24670.27684.5974-2.40694.00030.2150.0252-0.2423-0.1168-0.02480.16470.17740.1512-0.19020.07320.0012-0.07250.1102-0.01730.1032-1.71324.253-12.389
71.76520.15360.21591.6461-0.34652.62310.1908-0.0714-0.2343-0.002-0.01190.10680.0033-0.1016-0.17890.0788-0.0095-0.03370.10420.02690.0822-4.54227.031-6.712
85.9671-2.6632-9.63611.9672-2.740820.4537-0.10840.1583-0.05660.5929-0.14660.0598-0.3105-0.46190.2550.2165-0.0062-0.01290.3745-0.16020.2204-4.9240.4945.342
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 37
3X-RAY DIFFRACTION3A38 - 56
4X-RAY DIFFRACTION4A57 - 74
5X-RAY DIFFRACTION5A75 - 97
6X-RAY DIFFRACTION6A98 - 132
7X-RAY DIFFRACTION7A133 - 183
8X-RAY DIFFRACTION8A184 - 203

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