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- PDB-7dh8: Crystal structure of holo XcZur -

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Basic information

Entry
Database: PDB / ID: 7dh8
TitleCrystal structure of holo XcZur
ComponentsTranscriptional regulator fur family
KeywordsMETAL BINDING PROTEIN / Zinc perception / Conformational change / Zinc uptake regulator / DNA Binding
Function / homologyFerric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator fur family
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLiu, F.M. / Su, Z.H. / Chen, P. / Tian, X.L. / Wu, L.J. / Tang, D.J. / Li, P.F. / Deng, H.T. / Tang, J.L. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31700052 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis for zinc-induced activation of a zinc uptake transcriptional regulator.
Authors: Liu, F. / Su, Z. / Chen, P. / Tian, X. / Wu, L. / Tang, D.J. / Li, P. / Deng, H. / Ding, P. / Fu, Q. / Tang, J.L. / Ming, Z.
History
DepositionNov 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator fur family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6353
Polymers18,5041
Non-polymers1312
Water1,26170
1
A: Transcriptional regulator fur family
hetero molecules

A: Transcriptional regulator fur family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2706
Polymers37,0082
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2780 Å2
ΔGint-20 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.560, 122.900, 86.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

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Components

#1: Protein Transcriptional regulator fur family / Zinc-dependent zinc-uptake regulatory protein Zur


Mass: 18503.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain 8004) (bacteria)
Strain: 8004 / Gene: zur, XC_1430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4UWS5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→22.571 Å / Num. obs: 186417 / % possible obs: 95.5 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.35
Reflection shellResolution: 1.85→1.92 Å / Num. unique obs: 15557 / Rrim(I) all: 0.529

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→22.571 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 2867 9.97 %
Rwork0.2126 25880 -
obs0.2166 28747 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.43 Å2 / Biso mean: 49.7013 Å2 / Biso min: 18.7 Å2
Refinement stepCycle: final / Resolution: 1.85→22.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 2 70 1157
Biso mean--33.72 46.17 -
Num. residues----141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88190.48631490.4109138299
1.8819-1.91610.81191010.686389266
1.9161-1.95290.45761220.4954107579
1.9529-1.99280.31641530.301138899
1.9928-2.03610.27771460.2468134797
2.0361-2.08340.44871180.4283108782
2.0834-2.13550.29741580.2329137899
2.1355-2.19320.22871510.2148133698
2.1932-2.25760.37531270.3609114385
2.2576-2.33040.32181320.3082122287
2.3304-2.41360.231520.19051353100
2.4136-2.51020.26031500.2316136898
2.5102-2.62420.22821490.19481365100
2.6242-2.76240.30711530.2197136499
2.7624-2.93510.22431500.1745134099
2.9351-3.16120.19311560.1751368100
3.1612-3.47820.24481470.1913136398
3.4782-3.97920.25181520.18331353100
3.9792-5.00430.19371520.16291380100
5.0043-22.570.20691490.17261376100
Refinement TLS params.Method: refined / Origin x: 10.4417 Å / Origin y: 49.2423 Å / Origin z: 48.3738 Å
111213212223313233
T0.2403 Å2-0.0504 Å20.04 Å2-0.2281 Å2-0.0267 Å2--0.2825 Å2
L2.2127 °2-0.1934 °20.0824 °2-0.915 °2-0.7368 °2--2.514 °2
S-0.0328 Å °-0.0077 Å °-0.5313 Å °-0.1607 Å °-0.0411 Å °-0.0066 Å °0.308 Å °-0.0653 Å °0.0068 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 301
2X-RAY DIFFRACTION1allS1 - 70

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