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- PDB-5xm5: Crystal structure of Zinc binding protein ZinT at 1.49 Angstrom f... -

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Basic information

Entry
Database: PDB / ID: 5xm5
TitleCrystal structure of Zinc binding protein ZinT at 1.49 Angstrom from E. coli
ComponentsMetal-binding protein ZinT
KeywordsMETAL BINDING PROTEIN / Zinc binding protein
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.493 Å
AuthorsChen, J. / Wang, L. / Guo, J. / Xu, Y.
Funding support China, 3items
OrganizationGrant numberCountry
The National Natural Science Foundation of China31200556 China
the Program for Liaoning Excellent Talents in UniversityLJQ2015030 China
the Fundamental Research Funds for the Central UniversitiesDC201502020203 China
CitationJournal: To Be Published
Title: Crystal structure of Zinc binding protein ZinT at 1.49 Angstrom from E. coli
Authors: Chen, J. / Wang, L. / Guo, J. / Xu, Y.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.2Nov 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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-binding protein ZinT
B: Metal-binding protein ZinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,25513
Polymers44,7482
Non-polymers50711
Water9,350519
1
A: Metal-binding protein ZinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6397
Polymers22,3741
Non-polymers2656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-36 kcal/mol
Surface area10570 Å2
MethodPISA
2
B: Metal-binding protein ZinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6166
Polymers22,3741
Non-polymers2425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-35 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.021, 65.724, 73.532
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metal-binding protein ZinT / Cadmium-induced protein ZinT


Mass: 22373.879 Da / Num. of mol.: 2 / Fragment: UNP residue 24-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: zinT, yodA, b1973, JW1956
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P76344
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 22.5%(w/v) polyethylene glycol 4000, 0.135M ammonium acetate, and 0.1M sodium acetate trihydrate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Type: RIGAKU / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.493→31.228 Å / Num. obs: 56913 / % possible obs: 90.5 % / Redundancy: 2.2 % / Net I/σ(I): 13.319
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 16.37 / Num. unique obs: 54181 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
PHENIXphasing
HKL-2000data extraction
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4aw8

4aw8


Resolution: 1.493→31.228 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.18
RfactorNum. reflection% reflection
Rfree0.2338 2008 3.53 %
Rwork0.1791 --
obs0.181 56913 89.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.493→31.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 11 519 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113101
X-RAY DIFFRACTIONf_angle_d1.2494190
X-RAY DIFFRACTIONf_dihedral_angle_d13.8491140
X-RAY DIFFRACTIONf_chiral_restr0.074430
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4935-1.53080.34541170.32873154X-RAY DIFFRACTION73
1.5308-1.57220.37221280.30483499X-RAY DIFFRACTION80
1.5722-1.61850.311290.26563574X-RAY DIFFRACTION83
1.6185-1.67070.32861360.24623741X-RAY DIFFRACTION86
1.6707-1.73040.33211430.23543806X-RAY DIFFRACTION88
1.7304-1.79970.29911410.21873842X-RAY DIFFRACTION88
1.7997-1.88160.26441410.20523986X-RAY DIFFRACTION91
1.8816-1.98080.27361480.19094029X-RAY DIFFRACTION93
1.9808-2.10490.24771530.17254108X-RAY DIFFRACTION95
2.1049-2.26730.22661530.16664178X-RAY DIFFRACTION95
2.2673-2.49540.25151490.16574191X-RAY DIFFRACTION96
2.4954-2.85630.23371550.1714241X-RAY DIFFRACTION97
2.8563-3.59780.20981570.15924299X-RAY DIFFRACTION98
3.5978-31.23480.1711580.14714257X-RAY DIFFRACTION95

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