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- PDB-3fwz: Crystal structure of TrkA-N domain of inner membrane protein ybaL... -

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Basic information

Entry
Database: PDB / ID: 3fwz
TitleCrystal structure of TrkA-N domain of inner membrane protein ybaL from Escherichia coli
ComponentsInner membrane protein ybaL
KeywordsMEMBRANE PROTEIN / TrkA-N domain / ybaL / E.coli / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Antiport / Cell inner membrane / Cell membrane / Ion transport / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


: / potassium ion transport / membrane => GO:0016020 / nucleotide binding / plasma membrane
Similarity search - Function
K+/H+ exchanger / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...K+/H+ exchanger / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Putative cation/proton antiporter YbaL
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsChang, C. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of TrkA-N domain of inner membrane protein ybaL from Escherichia coli
Authors: Chang, C. / Bigelow, L. / Buck, K. / Joachimiak, A.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane protein ybaL
B: Inner membrane protein ybaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7335
Polymers31,0142
Non-polymers7193
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-45 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.801, 53.071, 72.537
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inner membrane protein ybaL


Mass: 15507.218 Da / Num. of mol.: 2 / Fragment: domain TrkA-N, residues 414-550
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b0478, Escherichia coli CFT073, JW0467, ybaL, ylaA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: P39830
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#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 / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 20% PEG3350, 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: 0.97926 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Dec 17, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 24693 / Num. obs: 24652 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 47
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 11.65 / Num. unique all: 620 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.51 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20159 1259 5.1 %RANDOM
Rwork0.16787 ---
all0.16968 24633 --
obs0.16968 24633 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.469 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20.13 Å2
2---0.77 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 47 201 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.472.0043072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35423.67398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40515392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6121523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211677
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.51408
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28422262
X-RAY DIFFRACTIONr_scbond_it2.2973844
X-RAY DIFFRACTIONr_scangle_it3.7064.5810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.786→1.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 77 -
Rwork0.16 1456 -
obs-1533 81.67 %
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)
11.5409-0.8860.1092.0768-0.35261.73420.03250.15980.0547-0.3454-0.0359-0.0514-0.0894-0.04290.00340.1174-0.02760.00540.04090.00990.017824.597727.15943.8738
20.6390.5694-0.20961.72140.59522.517-0.0467-0.0541-0.0679-0.11460.1098-0.07270.07630.1306-0.06310.0383-0.00990.01770.0332-0.01390.051129.743812.951151.1536
34.11973.92291.23443.98891.42851.62430.0787-0.0213-0.15450.0222-0.0387-0.1496-0.00560.0575-0.040.04390.00090.00750.06680.00610.099242.183624.525467.0503
40.9806-0.66320.40952.5792-0.55841.5518-0.0866-0.05540.05050.22540.0243-0.2021-0.0073-0.00550.06230.02320.007-0.01870.0152-0.00820.028737.075318.174682.059
51.3895-0.6116-0.04991.36310.31520.9592-0.0254-0.00310.0399-0.06790.07-0.0112-0.07250.0159-0.04460.0094-0.00550.0040.0151-0.0080.05730.117332.200875.0408
65.72370.6315-0.76842.95841.98975.3222-0.14020.17610.0446-0.10860.2476-0.1713-0.28120.2682-0.10740.0889-0.0549-0.00460.07520.00210.091436.630326.73755.1002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A416 - 489
2X-RAY DIFFRACTION2A490 - 535
3X-RAY DIFFRACTION3A536 - 550
4X-RAY DIFFRACTION4B416 - 489
5X-RAY DIFFRACTION5B490 - 535
6X-RAY DIFFRACTION6B536 - 548

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