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- PDB-1lyq: Crystal Structure of PcoC, a Methionine Rich Copper Resistance Pr... -

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Basic information

Entry
Database: PDB / ID: 1lyq
TitleCrystal Structure of PcoC, a Methionine Rich Copper Resistance Protein from Escherichia coli
ComponentsPcoC copper resistance protein
KeywordsMETAL BINDING PROTEIN / BETA BARREL / IG DOMAIN
Function / homology
Function and homology information


copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function
: / Copper transport protein C/D / CopC domain / CopC domain / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Copper resistance protein C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWernimont, A.K. / Huffman, D.L. / Finney, L.A. / Demeler, B. / O'Halloran, T.V. / Rosenzweig, A.C.
CitationJournal: J.BIOL.INORG.CHEM. / Year: 2003
Title: Crystal structure and dimerization equilibria of PcoC, a methionine-rich copper resistance protein from Escherichia coli
Authors: Wernimont, A.K. / Huffman, D.L. / Finney, L.A. / Demeler, B. / O'Halloran, T.V. / Rosenzweig, A.C.
History
DepositionJun 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PcoC copper resistance protein
B: PcoC copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5887
Polymers22,1272
Non-polymers4605
Water5,783321
1
A: PcoC copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4325
Polymers11,0641
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PcoC copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1562
Polymers11,0641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.123, 70.123, 39.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PcoC copper resistance protein / Copper resistance protein C


Mass: 11063.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: plasmid pRJ1004 / Plasmid: pDLHII265 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47454
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 81 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→35 Å / Num. all: 30640 / Num. obs: 29303 / % possible obs: 95.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.075 / Net I/σ(I): 6.2
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2399 / Rsym value: 0.278 / % possible all: 96.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb from MAD solution

Resolution: 1.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2926 -random
Rwork0.216 ---
all0.216 30640 --
obs0.216 29303 95.6 %-
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 30 321 1883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.8
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.247 370 -
Rwork0.242 --
obs-3658 95.5 %

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