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- PDB-8um6: Structure of copper bound to YcnI W137F -

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Basic information

Entry
Database: PDB / ID: 8um6
TitleStructure of copper bound to YcnI W137F
ComponentsUncharacterized protein YcnI
KeywordsMETAL BINDING PROTEIN / Cupredoxin / Copper-binding protein / DUF1775 / Histidine brace
Function / homologyYcnI-like / YcnI-like superfamily / Domain of unkown function (DUF1775) / plasma membrane / COPPER (II) ION / Copper-binding protein CutI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFisher, O.S. / Silva, Y.R.O. / Zheng, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2137107 United States
CitationJournal: J.Inorg.Biochem. / Year: 2024
Title: Stabilization of a Cu-binding site by a highly conserved tryptophan residue.
Authors: de Oliveira Silva, Y.R. / Zheng, D. / Peters, S.C. / Fisher, O.S.
History
DepositionOct 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein YcnI
B: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9374
Polymers28,8102
Non-polymers1272
Water2,990166
1
A: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4682
Polymers14,4051
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4682
Polymers14,4051
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.263, 90.263, 207.508
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

21B-383-

HOH

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Components

#1: Protein Uncharacterized protein YcnI


Mass: 14404.754 Da / Num. of mol.: 2 / Mutation: W137F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ycnI / Plasmid: pET28a+TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P94431
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 4.2 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M citric acid pH 3.5, 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.3776 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 1.95→103.75 Å / Num. obs: 37400 / % possible obs: 100 % / Redundancy: 38.1 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.052 / Rrim(I) all: 0.32 / Net I/av σ(I): 0.05 / Net I/σ(I): 5.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 36.9 % / Rmerge(I) obs: 1.112 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1811 / CC1/2: 0.774 / Rpim(I) all: 0.185 / Rrim(I) all: 1.127 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALS3.14.2data reduction
DIALS3.14.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.09 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 3717 5.39 %
Rwork0.2028 --
obs0.21 37333 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 0 167 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072083
X-RAY DIFFRACTIONf_angle_d0.7882849
X-RAY DIFFRACTIONf_dihedral_angle_d15.3581223
X-RAY DIFFRACTIONf_chiral_restr0.053306
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.36021320.33962365X-RAY DIFFRACTION98.7
1.97-20.32751400.33632430X-RAY DIFFRACTION99.8
2-2.030.37471320.34642416X-RAY DIFFRACTION99.9
2.03-2.060.34951390.31442438X-RAY DIFFRACTION100
2.06-2.090.33831340.31712376X-RAY DIFFRACTION100
2.09-2.120.36421320.29832430X-RAY DIFFRACTION100
2.12-2.160.33571390.28742435X-RAY DIFFRACTION100
2.16-2.190.30471380.27332429X-RAY DIFFRACTION100
2.19-2.230.31941400.27032385X-RAY DIFFRACTION100
2.23-2.270.26461420.25722427X-RAY DIFFRACTION100
2.28-2.320.29931420.25352403X-RAY DIFFRACTION100
2.32-2.370.25791410.23822438X-RAY DIFFRACTION100
2.37-2.430.30171360.2322387X-RAY DIFFRACTION100
2.43-2.490.29281400.23012439X-RAY DIFFRACTION100
2.49-2.560.32991310.23672411X-RAY DIFFRACTION100
2.56-2.630.23141350.23662398X-RAY DIFFRACTION100
2.63-2.720.30611370.23762415X-RAY DIFFRACTION100
2.72-2.810.26111390.23532424X-RAY DIFFRACTION100
2.81-2.920.25121420.23772422X-RAY DIFFRACTION100
2.92-3.060.25461400.21732405X-RAY DIFFRACTION100
3.06-3.220.27281360.19282423X-RAY DIFFRACTION100
3.22-3.420.21541410.17452408X-RAY DIFFRACTION100
3.42-3.680.19651360.15532413X-RAY DIFFRACTION100
3.68-4.050.17461310.14382438X-RAY DIFFRACTION100
4.06-4.640.16461420.12462404X-RAY DIFFRACTION100
4.64-5.840.16281380.13162426X-RAY DIFFRACTION100
5.84-39.090.17051420.18042430X-RAY DIFFRACTION100

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