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- PDB-5aq6: Structure of E. coli ZinT at 1.79 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5aq6
TitleStructure of E. coli ZinT at 1.79 Angstrom
ComponentsMETAL-BINDING PROTEIN ZINT
KeywordsMETAL BINDING PROTEIN / ZINC TRANSPORT / NATURAL HIS-TAG / METAL RESISTANCE
Function / homology
Function and homology information


cellular response to zinc ion starvation / intracellular zinc ion homeostasis / cadmium ion binding / cellular response to cadmium ion / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / zinc ion binding / metal ion binding / cytosol
Similarity search - Function
ZinT domain / ZinT (YodA) periplasmic lipocalin-like zinc-recruitment / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Metal-binding protein ZinT
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsSanto, P.E. / Colaco, H.G. / Matias, P. / Vicente, J.B. / Bandeiras, T.M.
CitationJournal: Metallomics / Year: 2016
Title: Roles of Escherichia Coli Zint in Cobalt, Mercury and Cadmium Resistance and Structural Insights Into the Metal Binding Mechanism
Authors: Colaco, H.G. / Santo, P.E. / Matias, P. / Bandeiras, T.M. / Vicente, J.B.
History
DepositionSep 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description
Category: atom_site / pdbx_database_status / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METAL-BINDING PROTEIN ZINT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,98510
Polymers22,4021
Non-polymers5839
Water3,225179
1
A: METAL-BINDING PROTEIN ZINT
hetero molecules

A: METAL-BINDING PROTEIN ZINT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,97120
Polymers44,8042
Non-polymers1,16718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2710 Å2
ΔGint-387.9 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.010, 62.010, 149.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein METAL-BINDING PROTEIN ZINT / CADMIUM-INDUCED PROTEIN ZINT / ZINT


Mass: 22401.955 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-216 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: ROSETTA / Strain: BL21(DE3) / References: UniProt: P76344
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE NUMBERED CONSIDERING MATURE PROTEIN. THE DEPOSITED PDB LACKS GLY2-HIS3-HIS4.

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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: 3.22 Å3/Da / Density % sol: 61.81 % / Description: NONE
Crystal growDetails: 75 MM ZINC ACETATE 18 % PEG 3350

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 2.1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.1 Å / Relative weight: 1
ReflectionResolution: 1.79→45.8 Å / Num. obs: 28379 / % possible obs: 99.6 % / Observed criterion σ(I): 1.7 / Redundancy: 6.7 % / Biso Wilson estimate: 24.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSPROGRAM PACKAGEdata reduction
XDSPROGRAM PACKAGEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.79→47.754 Å / SU ML: 0.17 / σ(F): 1.84 / Phase error: 20.66 / Stereochemistry target values: ML
Details: THE CLOSE CONTACTS BETWEEN THE ATOMS ZN1, ZN2, ZN3, ZN4, ZN6 AND ZN8 AND THE RESPECTIVE SIDE CHAINS ARE DUE TO COORDINATION DISTANCES.
RfactorNum. reflection% reflection
Rfree0.2083 1433 5.1 %
Rwork0.1746 --
obs0.1763 28294 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→47.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 12 179 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121642
X-RAY DIFFRACTIONf_angle_d1.3182227
X-RAY DIFFRACTIONf_dihedral_angle_d15.056604
X-RAY DIFFRACTIONf_chiral_restr0.051222
X-RAY DIFFRACTIONf_plane_restr0.006292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7901-1.8540.32621410.26792536X-RAY DIFFRACTION97
1.854-1.92830.2561350.23592649X-RAY DIFFRACTION100
1.9283-2.0160.2451310.19482633X-RAY DIFFRACTION100
2.016-2.12230.21931360.18422649X-RAY DIFFRACTION100
2.1223-2.25530.23091520.18392652X-RAY DIFFRACTION100
2.2553-2.42940.22451520.17282673X-RAY DIFFRACTION100
2.4294-2.67390.21031440.16612684X-RAY DIFFRACTION100
2.6739-3.06070.18291500.172703X-RAY DIFFRACTION100
3.0607-3.85590.19891480.15752762X-RAY DIFFRACTION100
3.8559-47.77130.18691440.16792920X-RAY DIFFRACTION100
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)
11.0348-0.23940.09970.76680.01060.44220.08370.3023-0.1362-0.1114-0.1836-0.04760.23440.1932-0.0420.18280.0494-0.00310.22480.00190.18856.946316.257922.0887
21.53220.15970.20931.7185-0.48450.80880.1366-0.00740.09290.4002-0.3471-0.1865-0.48070.8713-0.1330.1331-0.0944-0.09880.54280.07140.213771.455220.318440.7578
30.6274-0.2438-0.47310.7434-0.20330.9956-0.1156-0.13140.18020.1544-0.02140.0718-0.48150.335-0.13970.2624-0.1074-0.05410.26710.01880.20159.738526.031737.5371
40.1293-0.18430.0040.2380.11250.4734-0.0853-0.39180.08430.32710.2086-0.0216-0.4777-0.49510.00430.37310.0771-0.00010.2185-0.02680.280244.541829.882837.4893
50.1989-0.3296-0.04130.59430.16690.64060.17840.240.1302-0.1136-0.3092-0.0456-0.62030.2056-0.11590.2556-0.00450.01570.27510.08080.25252.156930.929822.784
61.7488-0.76160.40910.45360.22381.39650.0570.10020.108-0.0344-0.115-0.1564-0.11080.39940.00040.2013-0.0569-0.01550.19260.02460.200557.634522.900330.7929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 65 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 66 THROUGH 89 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 90 THROUGH 113 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 114 THROUGH 127 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 128 THROUGH 160 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 161 THROUGH 216 )

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