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- PDB-2r8d: The structure of transporter associated domain CorC_HlyC from a X... -

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Basic information

Entry
Database: PDB / ID: 2r8d
TitleThe structure of transporter associated domain CorC_HlyC from a Xylella fastidiosa Temecula1 hemolysin in complex with Mg++ and Mn++
ComponentsHemolysin
KeywordsTOXIN / CorC / hemolysin / structural genomics / pfam03471 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / membrane / metal ion binding
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsCuff, M.E. / Volkart, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of transporter associated domain CorC in complex with Mg++ and Mn++ from Xylella fastidiosa.
Authors: Cuff, M.E. / Volkart, L. / Joachimiak, A.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8343
Polymers10,7551
Non-polymers792
Water1,22568
1
A: Hemolysin
hetero molecules

A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6686
Polymers21,5092
Non-polymers1584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area1640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.061, 88.061, 88.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-92-

MN

DetailsAuthors state that the biological unit of this polypeptide is unknown, likely dimer.

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Components

#1: Protein Hemolysin


Mass: 10754.613 Da / Num. of mol.: 1 / Fragment: CorC_HlyC Domain: Residues 349-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: Temecula1 / Gene: tlyC / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q87DZ3
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 0.2M MgCl2, 20% PEG 8000, 5mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 9.9 / Number: 33510 / Rmerge(I) obs: 0.075 / Χ2: 1.9 / D res high: 2 Å / D res low: 50 Å / Num. obs: 7134 / % possible obs: 91.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.935099.310.0697.1415
3.914.9310010.0623.9955.3
3.423.9110010.0632.7275.4
3.113.4210010.061.5665.5
2.883.1110010.0721.1615.5
2.712.8810010.0951.0225.5
2.582.7110010.1220.8955.5
2.472.5810010.1480.8145.4
2.372.4799.610.1980.7795.3
2.292.379910.2380.6975
2.222.299910.2870.7054.2
2.152.229510.3530.7233.2
2.12.1581.610.3680.6742.3
2.052.160.310.4590.8111.6
22.0530.710.3560.5751.3
ReflectionResolution: 2→50 Å / Num. all: 7134 / Num. obs: 7134 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.902 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.356 / Num. unique all: 151 / Χ2: 0.575 / % possible all: 30.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.179 / FOM acentric: 0.198 / FOM centric: 0 / Reflection: 7134 / Reflection acentric: 6470 / Reflection centric: 664
Phasing MAD setR cullis acentric: 1.41 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 6470 / Reflection centric: 664
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.5-501.581.10.82114
7.14-12.51.280.80.611542
5-7.141.550.60.328662
3.85-51.180.40.352785
3.13-3.851.20.20.1849102
2.63-3.133.280.101261130
2.27-2.631.970.101731146
2-2.271.1300168083
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se62.92737-0.265-0.533-0.2010
2Se98.77704-0.274-0.633-0.0820
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.2910.4850352114
7.14-12.50.4420.604015711542
5-7.140.4390.535034828662
3.85-50.3810.443061252785
3.13-3.850.3490.3910951849102
2.63-3.130.2190.241013911261130
2.27-2.630.080.087018771731146
2-2.270.0150.01601763168083
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 7134
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.13-10057.50.846501
4.04-5.1358.30.925501
3.51-4.0458.90.896502
3.17-3.5159.80.883516
2.94-3.1761.50.854507
2.76-2.94600.874501
2.62-2.7670.60.878502
2.51-2.6270.40.868507
2.41-2.5178.60.868502
2.32-2.4176.70.882502
2.25-2.3281.80.85502
2.18-2.2589.20.84530
2.11-2.1885.60.819503
2-2.1189.70.624558

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→25.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.054 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 337 4.7 %RANDOM
Rwork0.171 ---
all0.173 7129 --
obs0.173 7129 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.58 Å2
Refinement stepCycle: LAST / Resolution: 2→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 0 2 68 706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022655
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.971887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.73423.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96315107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.481156
X-RAY DIFFRACTIONr_chiral_restr0.0940.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02499
X-RAY DIFFRACTIONr_nbd_refined0.1850.2309
X-RAY DIFFRACTIONr_nbtor_refined0.310.2446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.240
X-RAY DIFFRACTIONr_metal_ion_refined0.0050.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.25
X-RAY DIFFRACTIONr_mcbond_it1.2011.5404
X-RAY DIFFRACTIONr_mcangle_it1.4232623
X-RAY DIFFRACTIONr_scbond_it2.2593291
X-RAY DIFFRACTIONr_scangle_it3.3914.5263
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 9 -
Rwork0.267 179 -
all-188 -
obs--33.33 %
Refinement TLS params.Method: refined / Origin x: 23.6435 Å / Origin y: 41.4612 Å / Origin z: 10.5886 Å
111213212223313233
T-0.3476 Å20.034 Å2-0.0018 Å2--0.2472 Å20.0519 Å2---0.3122 Å2
L3.2223 °2-1.1919 °2-1.4603 °2-5.4709 °20.0242 °2--3.747 °2
S0.0269 Å °-0.5916 Å °0.0936 Å °0.6604 Å °0.3394 Å °-0.0143 Å °0.0107 Å °-0.075 Å °-0.3662 Å °

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