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- PDB-6lm2: Crystal structure of Zinc binding protein ZinT from E. coli -

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Basic information

Entry
Database: PDB / ID: 6lm2
TitleCrystal structure of Zinc binding protein ZinT from E. coli
ComponentsMetal-binding protein ZinT
KeywordsMETAL BINDING PROTEIN / Zinc binding protein ZinT from E. coli
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
: / Metal-binding protein ZinT
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13008410001 Å
AuthorsXiang, L. / Zhang, G. / Zhou, J.
CitationJournal: To Be Published
Title: Crystal structure of Zinc binding protein ZinT from E. coli
Authors: Xiang, L. / Zhang, G. / Zhou, J.
History
DepositionDec 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)21,8169
Polymers21,2931
Non-polymers5238
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-172 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.810, 55.810, 153.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

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Components

#1: Protein Metal-binding protein ZinT


Mass: 21292.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: 'BL21-Gold(DE3)pLysS AG' / References: UniProt: A0A3Z9V4E1, UniProt: P76344*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Zinc acetate, 0.1 M Sodium acetate pH 4.5, 10 %(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.13→45.13 Å / Num. obs: 14365 / % possible obs: 99.9 % / Redundancy: 24.6 % / Biso Wilson estimate: 36.7608797957 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.4
Reflection shellResolution: 2.13→2.19 Å / Num. unique obs: 1138 / CC1/2: 0.974

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YXC

5yxc


Resolution: 2.13008410001→38.355 Å / SU ML: 0.257544649448 / Cross valid method: FREE R-VALUE / σ(F): 1.34349736043 / Phase error: 31.5680159947
RfactorNum. reflection% reflection
Rfree0.27470515772 718 5.04638740512 %
Rwork0.225806772234 --
obs0.228154334809 14228 99.4130799329 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.7763735099 Å2
Refinement stepCycle: LAST / Resolution: 2.13008410001→38.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 8 38 1544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00707612701791536
X-RAY DIFFRACTIONf_angle_d0.8627272546642074
X-RAY DIFFRACTIONf_chiral_restr0.0495523658994213
X-RAY DIFFRACTIONf_plane_restr0.00471797324045269
X-RAY DIFFRACTIONf_dihedral_angle_d6.69981973997920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1301-2.29450.3463654579841240.3134075258122617X-RAY DIFFRACTION98.6326016553
2.2945-2.52540.3435130582771460.2693984829672623X-RAY DIFFRACTION99.0343347639
2.5254-2.89070.3215528274711690.2707896266822634X-RAY DIFFRACTION99.5737122558
2.8907-3.64160.3006367090761110.2297216326082753X-RAY DIFFRACTION99.8953610045
3.6416-38.3550.2245817556641680.1910064494412883X-RAY DIFFRACTION99.8690671031
Refinement TLS params.Method: refined / Origin x: 5.83049992863 Å / Origin y: 26.2568392815 Å / Origin z: 67.2037012503 Å
111213212223313233
T0.228938450088 Å2-0.0272779930551 Å2-0.0276932815943 Å2-0.184068704554 Å2-0.00466631505172 Å2--0.20686302597 Å2
L2.38202493213 °2-0.375556206918 °2-0.129277898413 °2-2.58611334946 °20.753121157763 °2--3.95807019622 °2
S0.209088437098 Å °-0.0960927316203 Å °0.0896634674344 Å °-0.131016577082 Å °-0.132764352896 Å °0.0544081160451 Å °-0.307686804033 Å °0.0260681029031 Å °-0.0615935445526 Å °
Refinement TLS groupSelection details: all

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