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- PDB-3jtf: The CBS Domain Pair Structure of a magnesium and cobalt efflux pr... -

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Basic information

Entry
Database: PDB / ID: 3jtf
TitleThe CBS Domain Pair Structure of a magnesium and cobalt efflux protein from Bordetella parapertussis in complex with AMP
ComponentsMagnesium and cobalt efflux protein
KeywordsTRANSPORT PROTEIN / CBS domain / CorC / AMP / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding
Similarity search - Function
CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain / CBS domain / CBS domain profile. ...CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain / CBS domain / CBS domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Magnesium and cobalt efflux protein
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Tesar, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The CBS Domain Pair Structure of a magnesium and cobalt efflux protein from Bordetella parapertussis in complex with AMP
Authors: Cuff, M.E. / Tesar, C. / Cobb, G. / Joachimiak, A.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 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: Magnesium and cobalt efflux protein
B: Magnesium and cobalt efflux protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6508
Polymers29,5712
Non-polymers1,0796
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-76 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.85, 84.85, 38.03
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Magnesium and cobalt efflux protein


Mass: 14785.486 Da / Num. of mol.: 2 / Fragment: sequence database residues 75-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Strain: 12822 / Gene: BPP1138, corC / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 / References: UniProt: Q7WB69
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium sulfate, 0.1M Bis Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942,0.97931
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979311
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 27.18 / Number: 97431 / Rmerge(I) obs: 0.1 / Χ2: 1.34 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 13225 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.15010010.0533.467
4.856.110010.0562.3627.1
4.234.8510010.0522.0137.2
3.854.2310010.0642.2077.3
3.573.8510010.0721.8647.4
3.363.5710010.0811.3557.4
3.193.3610010.0981.1787.5
3.053.1910010.1211.1597.4
2.943.0510010.1311.0167.4
2.832.9410010.161.0357.5
2.752.8310010.2020.9947.5
2.672.7510010.2520.9437.5
2.62.6710010.2840.937.5
2.532.610010.3340.927.5
2.482.5310010.3560.9167.4
2.422.4810010.3910.8757.5
2.382.4210010.5170.9447.5
2.332.3810010.5550.877.4
2.292.3310010.6080.8447.3
2.252.2910010.6140.857.2
ReflectionResolution: 2→50 Å / Num. all: 18585 / Num. obs: 18585 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.894 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.038.10.5028970.7441100
2.03-2.078.20.4059350.821100
2.07-2.118.40.3519240.8481100
2.11-2.158.20.3219080.8691100
2.15-2.28.30.2799050.9361100
2.2-2.258.40.2329490.9311100
2.25-2.318.20.2168871.0311100
2.31-2.378.40.2039771.0281100
2.37-2.448.20.1818921.1941100
2.44-2.528.40.1589351.2721100
2.52-2.618.20.1549141.4171100
2.61-2.718.50.1369401.4651100
2.71-2.848.10.1179291.6311100
2.84-2.998.30.1059201.8611100
2.99-3.178.30.0999452.0731100
3.17-3.428.20.0929212.491100
3.42-3.768.10.0869422.961100
3.76-4.317.90.0789473.575199.8
4.31-5.437.90.0739553.816199.6
5.43-507.40.0939637.49197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2→32.12 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.892 / SU B: 8.068 / SU ML: 0.107 / SU R Cruickshank DPI: 0.184 / SU Rfree: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.163
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 950 5.1 %RANDOM
Rwork0.175 ---
all0.177 18566 --
obs0.177 18566 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 141.74 Å2 / Biso mean: 23.722 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 66 156 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222150
X-RAY DIFFRACTIONr_bond_other_d0.0010.021500
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.0372937
X-RAY DIFFRACTIONr_angle_other_deg0.93333643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4025266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90221.95997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3915396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5491531
X-RAY DIFFRACTIONr_chiral_restr0.0910.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_mcbond_it1.0141.51276
X-RAY DIFFRACTIONr_mcbond_other0.241.5502
X-RAY DIFFRACTIONr_mcangle_it1.88922096
X-RAY DIFFRACTIONr_scbond_it2.7853874
X-RAY DIFFRACTIONr_scangle_it4.4914.5831
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 56 -
Rwork0.199 1250 -
all-1306 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.02271.52010.20363.03451.09942.5325-0.0802-0.2178-0.0682-0.1193-0.02430.0548-0.10380.05680.10450.03390.0298-0.02060.06530.01290.045421.754131.812326.8874
21.18520.4363-0.05881.37210.60961.29420.0140.0082-0.05440.039-0.0109-0.03090.05250.0068-0.0030.02470.0084-0.00420.02450.01480.01566.996536.935443.3664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 199
2X-RAY DIFFRACTION1A1 - 3
3X-RAY DIFFRACTION1A7 - 235
4X-RAY DIFFRACTION2B75 - 199
5X-RAY DIFFRACTION2B1 - 5
6X-RAY DIFFRACTION2B2 - 253

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