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- PDB-3ced: Crystal structure of the C-terminal NIL domain of an ABC transpor... -

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Basic information

Entry
Database: PDB / ID: 3ced
TitleCrystal structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus
ComponentsMethionine import ATP-binding protein metN 2
KeywordsHYDROLASE / ABC transporter / NIL domain / Staphylococcus aureus / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Amino-acid transport / ATP-binding / Membrane / Nucleotide-binding
Function / homology
Function and homology information


ABC-type methionine transporter / ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / ACT domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / ACT domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / Methionine import ATP-binding protein MetN 2
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsCuff, M.E. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus.
Authors: Cuff, M.E. / Bigelow, L. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: 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

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Assembly

Deposited unit
A: Methionine import ATP-binding protein metN 2
B: Methionine import ATP-binding protein metN 2
C: Methionine import ATP-binding protein metN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4197
Polymers33,0583
Non-polymers3604
Water5,819323
1
A: Methionine import ATP-binding protein metN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2003
Polymers11,0191
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine import ATP-binding protein metN 2


Theoretical massNumber of molelcules
Total (without water)11,0191
Polymers11,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionine import ATP-binding protein metN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2003
Polymers11,0191
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.550, 132.550, 132.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

21C-431-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein Methionine import ATP-binding protein metN 2


Mass: 11019.340 Da / Num. of mol.: 3 / Fragment: NIL domain: Residues 247-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: Mu50 / Gene: metN2, SAV0837 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99VG8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% 1,4-Butanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionRedundancy: 16.3 % / Av σ(I) over netI: 8.2 / Number: 526788 / Rmerge(I) obs: 0.087 / Χ2: 1.46 / D res high: 2.15 Å / D res low: 50 Å / Num. obs: 32344 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.18509910.0573.69415.3
4.115.1810010.0552.62115.7
3.594.1110010.072.68216
3.263.5910010.0752.04616.3
3.033.2610010.0891.57216.4
2.853.0310010.1081.29816.4
2.712.8510010.1391.05516.5
2.592.7110010.1750.9716.5
2.492.5910010.2090.88316.5
2.412.4910010.2530.79716.6
2.332.4110010.2960.76516.5
2.262.3310010.3470.74316.5
2.22.2610010.4250.69316.5
2.152.210010.4630.68716.5
ReflectionResolution: 2.15→50 Å / Num. all: 32344 / Num. obs: 32344 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16.3 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.46 / Net I/σ(I): 8.2
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2279 / Χ2: 0.687 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.15 Å / D res low: 50 Å / FOM : 0.413 / FOM acentric: 0.428 / FOM centric: 0.285 / Reflection: 32206 / Reflection acentric: 28941 / Reflection centric: 3265
Phasing MAD set

Highest resolution: 2.15 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.9710.20.100289413265
20.910.881420.80.730.56270823118
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
113.22-501.2710.60.5008567
17.62-13.221.2810.60.400469174
15.35-7.621.9810.50.3001158271
14.12-5.351.3310.40.3002178357
13.35-4.121.3410.30.2003502459
12.83-3.351.8810.20.1005137553
12.44-2.833.6610.20007059643
12.15-2.445.6410.10009353741
213.22-500.820.819.929.11.690.938563
27.62-13.220.770.719.424.91.571.11469174
25.35-7.620.740.7616.121.71.611.011158271
24.12-5.350.840.8219.2251.050.722178357
23.35-4.120.910.8919.424.70.770.563502459
22.83-3.350.910.9413.720.60.750.435137553
22.44-2.830.950.9611.216.70.60.357057643
22.15-2.440.990.9912.217.30.360.237496598
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se31.78432-0.896-0.629-0.1940
2Se31.75774-1.104-0.695-0.1280
3Se44.68042-1.128-0.806-0.1040
4Se32.02475-0.896-0.629-0.194-0.139
5Se27.9407-1.104-0.694-0.129-0.119
6Se43.56807-1.128-0.806-0.104-0.114
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
13.22-500.5920.7170.4351528567
7.62-13.220.6990.7610.53643469174
5.35-7.620.720.770.50714291158271
4.12-5.350.6660.7020.44525352178357
3.35-4.120.5950.6270.3539613502459
2.83-3.350.5270.5530.2956905137553
2.44-2.830.370.3860.19977027059643
2.15-2.440.1830.1910.085100949353741

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.004data 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: MAD / Resolution: 2.15→35.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.053 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1632 5.1 %RANDOM
Rwork0.184 ---
all0.186 32204 --
obs0.186 32204 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 24 323 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222452
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9863324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0325314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23425.385104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90215457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.389159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021794
X-RAY DIFFRACTIONr_nbd_refined0.1920.2917
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.227
X-RAY DIFFRACTIONr_mcbond_it1.1061.51578
X-RAY DIFFRACTIONr_mcangle_it1.56722482
X-RAY DIFFRACTIONr_scbond_it2.4183987
X-RAY DIFFRACTIONr_scangle_it3.9684.5834
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 117 -
Rwork0.184 2233 -
all-2350 -
obs--99.96 %
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)
12.84780.0717-0.18071.88720.37471.81720.1246-0.1074-0.01470.04760.01060.0707-0.09370.0232-0.1352-0.0937-0.02450.0021-0.0716-0.0192-0.046251.559223.116741.0123
21.7436-0.01730.43072.75560.08531.8956-0.12280.08030.02580.02240.10940.1290.0694-0.04060.0134-0.0478-0.0036-0.0172-0.09370.0249-0.069325.122951.629543.0665
31.6479-0.47170.10071.36020.11742.5970.0002-0.0537-0.0677-0.0436-0.135-0.07420.1338-0.03520.1348-0.06850.01420.0244-0.04630.004-0.085423.023125.113114.685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA244 - 3411 - 98
2X-RAY DIFFRACTION2BB244 - 3411 - 98
3X-RAY DIFFRACTION3CC244 - 3411 - 98

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