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- PDB-7dh7: Crystal structure of apo XcZur -

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Basic information

Entry
Database: PDB / ID: 7dh7
TitleCrystal structure of apo XcZur
ComponentsTranscriptional regulator fur family
KeywordsMETAL BINDING PROTEIN / Zinc perception / Conformational change / Zinc uptake regulator / DNA Binding
Function / homology
Function and homology information


regulation of secondary metabolite biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytosol
Similarity search - Function
Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Transcriptional regulator fur family
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.2May 29, 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
B: Transcriptional regulator fur family
C: Transcriptional regulator fur family
D: Transcriptional regulator fur family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,75213
Polymers74,0164
Non-polymers7369
Water6,107339
1
A: Transcriptional regulator fur family
C: Transcriptional regulator fur family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3296
Polymers37,0082
Non-polymers3214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-21 kcal/mol
Surface area15060 Å2
MethodPISA
2
B: Transcriptional regulator fur family
D: Transcriptional regulator fur family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4247
Polymers37,0082
Non-polymers4165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-21 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.391, 77.871, 73.063
Angle α, β, γ (deg.)90.000, 103.070, 90.000
Int Tables number5
Space group name H-MC121

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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.: 4
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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 18% w/v polyethylene glycol 8,000, 0.3 M glycyl-glycyl-glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42394 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.01
Reflection shellResolution: 2.2→2.34 Å / Rmerge(I) obs: 0.387 / Num. unique obs: 6926

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.94 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 2029 4.79 %RANDOM
Rwork0.2194 40360 --
obs0.2221 42389 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.83 Å2 / Biso mean: 40.1452 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 2.2→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 29 339 4914
Biso mean--49.95 40.34 -
Num. residues----596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.32121230.27392755287896
2.26-2.320.31481460.246628613007100
2.32-2.390.30831630.241628513014100
2.39-2.460.321470.247928963043100
2.46-2.550.3191500.233528543004100
2.55-2.650.28841380.247429043042100
2.65-2.770.29061510.23628813032100
2.77-2.920.31881480.248828903038100
2.92-3.10.30981360.228128873023100
3.1-3.340.26651340.216829263060100
3.34-3.680.25771670.196828813048100
3.68-4.210.23161390.19328933032100
4.21-5.30.21551620.180429153077100
5.3-38.940.30151250.22592966309199
Refinement TLS params.Method: refined / Origin x: 51.2005 Å / Origin y: 8.1719 Å / Origin z: 21.7363 Å
111213212223313233
T0.0932 Å2-0.0129 Å20.0495 Å2-0.1364 Å2-0.0688 Å2--0.0587 Å2
L1.6931 °2-0.104 °2-0.0003 °2-1.311 °2-0.0284 °2--2.0599 °2
S-0.181 Å °0.0752 Å °-0.0212 Å °-0.0357 Å °0.2901 Å °-0.206 Å °-0.0274 Å °-0.2337 Å °-0.0469 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 170
2X-RAY DIFFRACTION1allA176
3X-RAY DIFFRACTION1allB22 - 169
4X-RAY DIFFRACTION1allB176
5X-RAY DIFFRACTION1allC21 - 170
6X-RAY DIFFRACTION1allC176
7X-RAY DIFFRACTION1allD22 - 171
8X-RAY DIFFRACTION1allD176
9X-RAY DIFFRACTION1allG1 - 5
10X-RAY DIFFRACTION1allS1 - 339

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