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- PDB-3lvu: Crystal structure of ABC transporter, periplasmic substrate-bindi... -

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Basic information

Entry
Database: PDB / ID: 3lvu
TitleCrystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi
ComponentsABC transporter, periplasmic substrate-binding proteinATP-binding cassette transporter
KeywordsTRANSPORT PROTEIN / MCSG / PSI-2 / ABC transporter / periplasmic substrate-binding protein / Silicibacter pomeroyi / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / ABC transporter, periplasmic substrate-binding protein
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsChang, C. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi
Authors: Chang, C. / Chhor, G. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,26128
Polymers114,5414
Non-polymers2,72024
Water13,079726
1
A: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1085
Polymers28,6351
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,84012
Polymers28,6351
Non-polymers1,20411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1706
Polymers28,6351
Non-polymers5355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1435
Polymers28,6351
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.384, 75.517, 78.477
Angle α, β, γ (deg.)82.63, 80.29, 77.42
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ABC transporter, periplasmic substrate-binding protein / ATP-binding cassette transporter


Mass: 28635.301 Da / Num. of mol.: 4 / Fragment: sequence database residues 314-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO2066 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5LRQ9

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Non-polymers , 5 types, 750 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium iodide, 20% PEG3350, pH 6.5, 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: 0.97901 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 97131 / Num. obs: 94748 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.37 / Num. unique all: 2293 / % possible all: 96.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.401 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20476 4666 5 %RANDOM
Rwork0.16905 ---
all0.17084 93537 --
obs0.17084 93537 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.701 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0.36 Å20.88 Å2
2---0.08 Å20.03 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7977 0 76 726 8779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228531
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.97111600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30151095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.92722.388423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.772151354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4815115
X-RAY DIFFRACTIONr_chiral_restr0.0970.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216759
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_it0.8421.55327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51228531
X-RAY DIFFRACTIONr_scbond_it2.54833204
X-RAY DIFFRACTIONr_scangle_it4.0214.53069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 295 -
Rwork0.271 5863 -
obs-6158 84.93 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.7321-0.0213-0.03890.9533-0.38772.1944-0.07360.1110.0685-0.09860.0413-0.008-0.0259-0.120.03240.0669-0.03310.01390.037-0.00610.029848.637361.679430.3775
21.33761.030.59781.46440.20682.3491-0.04040.0314-0.0196-0.0735-0.0075-0.1163-0.33330.04510.04790.0852-0.01240.01680.00780.00480.044854.602275.615838.8108
30.86850.0767-0.4020.594-0.80081.6956-0.08910.0784-0.0611-0.14410.0574-0.0340.1953-0.05740.03160.1029-0.04090.02030.0321-0.02410.020449.590853.657626.5097
41.13840.42730.25881.36560.11680.89990.0001-0.07830.02990.0181-0.0238-0.05-0.0952-0.06640.02370.0475-0.00130.00470.0484-0.00190.039550.613267.872446.7408
51.2458-0.5054-0.49691.28280.08520.53210.0051-0.06160.0342-0.08880.0398-0.09560.00180.1053-0.04490.0127-0.00450.01420.0929-0.00050.072868.071976.9075-6.3962
62.98890.49380.01190.96930.4242.0865-0.11820.0024-0.0962-0.0688-0.04940.0360.08590.03440.16760.03710.02320.0150.01740.0030.058154.868164.8065-6.2308
70.8054-0.428-0.46361.51650.54531.67560.0142-0.03780.1305-0.11350.114-0.2318-0.11080.2566-0.12820.0145-0.0250.01990.09680.00890.099972.381483.658-9.7595
80.46370.2950.04041.94590.17590.99440.0290.0028-0.02820.042-0.06470.1949-0.0457-0.02490.03570.01030.0157-0.00670.065-0.01090.067751.356975.1362-0.6082
91.21840.0384-0.63061.50660.36290.82650.01130.0466-0.030.056-0.04340.09710.0199-0.05620.03210.0320.01580.00030.05550.00470.062360.887139.5459-15.4989
101.4887-0.9921-0.39971.90120.87351.4836-0.110.0156-0.11390.21880.02660.15490.0383-0.03140.08340.0492-0.00770.01350.01950.01910.050468.455323.8143-15.8326
111.76440.6651-0.73781.0172-0.32011.25080.12840.00030.14150.1346-0.00450.1218-0.0832-0.0427-0.12390.04550.02310.01730.02150.00090.038359.664547.3515-11.5705
120.5787-0.2830.0941.66860.1010.8848-0.02350.0337-0.0509-0.0290.0764-0.11460.0105-0.0111-0.05290.03250.0018-0.00390.06670.01420.056375.173231.1399-21.8185
130.9491-0.5453-0.29971.65050.62242.5413-0.0944-0.09160.0330.230.0707-0.02280.09210.19090.02360.10550.0045-0.00650.04460.00080.015636.85225.541624.3456
141.2382-0.62560.05222.614-0.62632.28780.1205-0.03820.06230.031-0.03910.0001-0.26630.075-0.08140.0694-0.02360.01050.012-0.00910.020537.345140.872915.7146
150.9313-0.0769-0.06161.29811.411.8684-0.0726-0.0371-0.07810.3352-0.01490.09990.2946-0.00850.08750.1659-0.01770.02860.03760.02720.033632.844918.672227.9994
160.8356-0.1931-0.36791.77040.12170.67020.04770.04160.0398-0.1192-0.0302-0.0422-0.09780.0233-0.01750.0766-0.0016-0.00640.0484-0.00850.027437.856432.02847.9179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A311 - 354
2X-RAY DIFFRACTION2A355 - 398
3X-RAY DIFFRACTION3A399 - 493
4X-RAY DIFFRACTION4A494 - 568
5X-RAY DIFFRACTION5B311 - 354
6X-RAY DIFFRACTION6B355 - 398
7X-RAY DIFFRACTION7B399 - 493
8X-RAY DIFFRACTION8B494 - 568
9X-RAY DIFFRACTION9C311 - 354
10X-RAY DIFFRACTION10C355 - 398
11X-RAY DIFFRACTION11C399 - 493
12X-RAY DIFFRACTION12C494 - 568
13X-RAY DIFFRACTION13D311 - 354
14X-RAY DIFFRACTION14D355 - 398
15X-RAY DIFFRACTION15D399 - 493
16X-RAY DIFFRACTION16D494 - 568

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