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- PDB-3is6: The Crystal Structure of a domain of a putative Permease protein ... -

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Basic information

Entry
Database: PDB / ID: 3is6
TitleThe Crystal Structure of a domain of a putative Permease protein from Porphyromonas gingivalis to 2A
Componentsputative permease protein, ABC transporter
KeywordsTRANSPORT PROTEIN / ABC / transporter / permease / porphyromonas / gingivalis / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative / Cell membrane / Membrane / Transmembrane
Function / homologyMacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC3 transporter permease protein domain / FtsX-like permease family / membrane => GO:0016020 / plasma membrane / ABC transporter, permease protein, putative
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsStein, A.J. / Sather, A. / Duggan, E. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a domain of a putative Permease protein from Porphyromonas gingivalis to 2A
Authors: Stein, A.J. / Sather, A. / Duggan, E. / Moy, S. / Joachimiak, A.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative permease protein, ABC transporter
B: putative permease protein, ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3014
Polymers56,0832
Non-polymers2182
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-30 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.390, 79.193, 105.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative permease protein, ABC transporter


Mass: 28041.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pMCSG8 / Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG0684, PG_0684 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MWD8
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 3000, 0.1M Tris pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 39970 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.101 / Χ2: 2.649 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.0250.71739550.971100
2.02-2.150.50339220.976199.9
2.1-2.250.3639461.0291100
2.2-2.3150.25839591.1071100
2.31-2.4650.20239451.2371100
2.46-2.6550.15639701.4671100
2.65-2.9150.1240042.092199.9
2.91-3.334.90.09540083.231100
3.33-4.24.90.07940455.163199.9
4.2-504.60.08242169.562199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.95→43.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.212 / SU B: 9.087 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1994 5 %RANDOM
Rwork0.213 ---
obs0.215 39858 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 13 189 3656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223535
X-RAY DIFFRACTIONr_bond_other_d0.0170.0212
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.984798
X-RAY DIFFRACTIONr_angle_other_deg1.692324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61923.172145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9891531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212633
X-RAY DIFFRACTIONr_mcbond_it0.571.52266
X-RAY DIFFRACTIONr_mcbond_other0.1991.53
X-RAY DIFFRACTIONr_mcangle_it1.0523635
X-RAY DIFFRACTIONr_scbond_it2.24531269
X-RAY DIFFRACTIONr_scangle_it3.2854.51161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.947-1.9970.2841360.2492648290295.934
1.997-2.0520.281340.2392693283799.648
2.052-2.1110.2931520.2362582274499.636
2.111-2.1760.2791390.2292543269199.666
2.176-2.2470.2941290.2332501263399.886
2.247-2.3260.2381320.21523892521100
2.326-2.4130.315940.2132336243299.918
2.413-2.5120.2641230.2082240236499.958
2.512-2.6230.2971040.2372159226499.956
2.623-2.750.2721110.2342058217399.816
2.75-2.8990.2751050.241943205099.902
2.899-3.0740.31070.2281872198199.899
3.074-3.2850.254850.21917641849100
3.285-3.5460.2311030.1991613171999.825
3.546-3.8820.193730.1831519159599.812
3.882-4.3360.201600.18313931453100
4.336-4.9990.257650.181248131499.924
4.999-6.1020.249630.2191045110999.91
6.102-8.5470.299530.22982788299.773
8.547-43.7830.305260.23949154694.689
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)
14.1486-1.76280.4345.0677-2.90633.534-0.0037-0.3295-0.4460.43620.03420.1550.2947-0.1075-0.03050.2357-0.0867-0.01480.21140.01760.11.53818.828820.4039
211.387-8.20227.74895.9273-5.42436.8937-0.15950.12030.02450.0973-0.06970.003-0.3187-0.20950.22920.37690.0135-0.04780.4684-0.04990.4688-16.220631.948611.2215
32.6088-0.9841-0.18852.6357-0.40071.4962-0.0154-0.33930.12850.3376-0.05810.0558-0.0791-0.1130.07350.0929-0.0490.01050.1768-0.04740.0799-0.358724.551620.0205
48.0418-5.5386-3.9053.95282.0215.71750.31460.29110.5783-0.1702-0.1001-0.3916-0.2097-0.1677-0.21450.19640.0130.04120.3370.01140.208312.182521.139-1.3144
55.4743-0.1051-6.0310.01850.19977.34380.00520.083-0.181-0.0067-0.0246-0.03330.0283-0.0740.01950.07140.03060.00950.12680.01430.133618.35317.3573-0.9553
63.46135.69740.29529.39210.36384.35780.1554-0.1882-0.01110.2664-0.2727-0.02150.12970.17630.11730.1515-0.0226-0.03540.23920.03750.13210.664614.680618.9447
79.4363-1.21590.70322.82613.4744.83410.0426-0.3952-0.26330.33810.007-0.03590.4272-0.0269-0.04950.2209-0.0489-0.08730.30430.13530.25220.532712.111417.0639
85.7792.7365-1.00187.76740.56766.32310.1316-0.37310.25530.0582-0.2253-0.1662-0.33150.28290.09370.06250.0213-0.04460.19740.03520.121619.731917.44710.5216
918.904-6.255-10.752.60832.18399.8006-0.1168-0.28870.2113-0.1278-0.0492-0.26470.41530.55960.16590.21830.03380.02920.2188-0.03250.36521.687.68291.1502
105.6062-2.22792.98111.5672-7.13110.31340.0139-0.1639-0.01160.1203-0.0255-0.0059-0.05650.38290.01150.03470.0147-0.00650.1943-0.00850.090224.851319.1551.1964
111.3641-0.03090.42578.0675-3.72811.85640.2258-0.1320.02710.1304-0.13930.1591-0.01480.0509-0.08650.1777-0.00860.03080.2054-0.02480.157524.806724.58572.3403
127.35322.84870.40231.11970.0590.63670.1865-0.3449-0.71650.0186-0.1346-0.27320.3394-0.0902-0.05180.2089-0.0327-0.04770.17360.02450.1568.8168.19839.8161
134.64172.6612-0.70839.41982.36836.1730.0880.0594-0.0197-0.363-0.0837-0.3047-0.1140.1775-0.00430.05390.004-0.02640.1420.05620.126212.658719.27559.1574
1415.2907-6.1324-8.93042.51773.81187.59830.139-0.16710.4614-0.1067-0.0227-0.1546-0.37150.0717-0.11630.2909-0.05940.00280.2375-0.02480.33177.888632.594714.8439
151.0298-2.86840.01178.50681.35754.1077-0.0127-0.0320.035-0.0567-0.03680.0229-0.4462-0.2350.04940.239-0.02230.040.2228-0.03980.31590.86429.204612.0833
162.3936-1.7019-0.24453.9779-0.33951.8758-0.1941-0.5302-0.19740.53510.17820.35820.0759-0.11310.01590.2672-0.04780.04480.3627-0.01060.127-4.797419.170127.9214
1713.98314.6498-4.948918.2979-1.34467.83070.2718-0.50840.16680.39330.00560.1728-0.17340.1421-0.27740.1989-0.04660.01180.2637-0.1340.1936-4.374534.074726.7995
1844.13856.6540.884731.619315.062940.4668-2.0859-0.88071.80570.5072-0.02121.2662-1.8002-0.76742.10710.5214-0.0872-0.27670.5111-0.0631.2027-8.761840.59317.944
191.725-0.38280.0162.88471.25062.3566-0.017-0.09780.12350.1309-0.1910.5357-0.2211-0.35150.2080.1192-0.04490.01080.2223-0.03680.1561-7.855222.441117.1952
202.36430.21120.13890.6482.08276.84350.07420.2776-0.31670.08830.05-0.0660.26310.1774-0.12410.24090.0092-0.02010.2383-0.03020.30360.0112.2007-2.7248
215.7358-0.3373-0.5074.29263.99286.18980.0631-0.08280.06660.1379-0.1570.3227-0.0941-0.44090.09390.25890.1493-0.04950.24850.00890.1574.907452.207-2.3887
2222.785629.974824.747839.660734.314242.5999-0.1025-0.5033-0.0756-0.2508-0.7940.1424-0.0097-2.32530.89650.47510.0757-0.2230.6173-0.05640.80087.058435.84-7.6437
235.0036-3.0770.04136.0414-4.40224.63630.49940.42330.195-0.0412-0.33210.0841-0.23440.1415-0.16730.39650.16140.03630.28030.04030.19815.164349.1634-13.0525
242.9508-1.92731.92454.5642-3.215.98760.0623-0.03130.1976-0.0135-0.07410.0432-0.4039-0.16620.01170.17090.06540.03540.0834-0.01690.093817.223946.8661-0.3963
2516.01543.14591.26576.0650.01844.50020.2074-0.35720.14260.38490.1436-0.62280.01670.294-0.3510.25290.0064-0.04950.303-0.03850.226628.763444.87621.2309
263.5025-1.02552.60279.1199-3.760718.17820.2772-0.12180.097-0.26130.01270.2564-0.04750.1183-0.28990.08060.0230.05050.0606-0.01220.106720.336746.17696.588
274.4421-1.8709-2.60931.10031.26314.96520.22490.3380.3985-0.4472-0.2169-0.0402-0.8967-0.1334-0.0080.55470.0854-0.05470.12890.03090.279415.322856.7833.4258
280.4482-0.72520.02883.3114.809712.34970.0910.10740.351-0.6373-0.3309-0.3462-0.8035-0.23580.23990.4633-0.02130.13770.22480.02990.48723.09861.18247.133
298.51260.0258-5.2664.03921.015211.16850.198-0.04950.517-0.17810.0952-0.2322-0.47630.2359-0.29330.1588-0.01870.05060.0874-0.00620.173624.035753.283611.9946
3010.3468-2.116-4.76531.1632.70426.2951-0.003-0.79560.2553-0.02670.1337-0.0639-0.06020.3315-0.13070.286-0.08720.06670.3523-0.02660.248326.217954.695220.9872
314.4881-2.9605-0.16917.51541.92695.21920.168-0.17210.00510.15430.3722-0.75270.34790.8929-0.54020.1667-0.015-0.02060.3122-0.10120.26132.982546.968314.0125
3210.42461.12263.65897.37334.1876.37540.2346-0.41590.2692-0.1787-0.43120.3016-0.1891-0.54770.19670.12720.02810.0510.1771-0.01520.077811.152950.017711.5143
336.933-1.7791-6.62593.45954.94949.8650.1892-0.1895-0.0392-0.10480.1037-0.349-0.25990.2513-0.29290.2257-0.01580.05420.15380.02340.288924.439248.57774.5001
345.15710.86622.39895.6872.51611.92320.0760.277-0.0266-0.47350.0055-0.1684-0.16810.1185-0.08150.27950.0190.11380.21860.01690.189727.251342.2093-5.2558
355.8799-4.4461.19355.1908-1.22771.7990.10030.17870.1036-0.2374-0.18830.1312-0.2271-0.18440.0880.20890.11090.00460.1476-0.02110.110312.239146.9373-7.9592
366.1658-7.024-2.72659.14114.18186.38590.05470.2876-0.0584-0.6036-0.10320.34810.31230.00610.04850.63110.1422-0.16240.44420.00770.21318.940645.2862-19.1847
370.0232-0.153-0.18011.0741.26811.49960.0385-0.0139-0.0261-0.52220.0891-0.0612-0.58550.1338-0.12760.95780.0956-0.0420.7348-0.14350.961215.198535.1155-18.9557
387.2884-6.8973-7.09949.967710.337619.28110.02080.5978-0.3524-0.3928-0.50710.66020.361-1.00080.48630.29670.0929-0.11240.2894-0.03710.1965.6443.7845-9.3087
3911.6313-13.4789-1.384417.47913.47072.05320.4013-0.1122-0.5403-0.3678-0.54650.6828-0.0097-0.63990.14520.47590.04330.07210.50090.04880.53557.394737.31643.1463
4015.33691.56523.022218.86363.09319.39470.044-0.52030.6276-0.14310.13050.2198-0.3392-0.5206-0.17450.17520.01520.07780.11430.0060.224318.843532.43325.7344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 58
2X-RAY DIFFRACTION2A59 - 72
3X-RAY DIFFRACTION3A73 - 103
4X-RAY DIFFRACTION4A104 - 109
5X-RAY DIFFRACTION5A110 - 124
6X-RAY DIFFRACTION6A125 - 134
7X-RAY DIFFRACTION7A135 - 145
8X-RAY DIFFRACTION8A146 - 156
9X-RAY DIFFRACTION9A157 - 164
10X-RAY DIFFRACTION10A165 - 174
11X-RAY DIFFRACTION11A175 - 185
12X-RAY DIFFRACTION12A186 - 196
13X-RAY DIFFRACTION13A197 - 205
14X-RAY DIFFRACTION14A206 - 215
15X-RAY DIFFRACTION15A216 - 222
16X-RAY DIFFRACTION16A223 - 241
17X-RAY DIFFRACTION17A242 - 248
18X-RAY DIFFRACTION18A249 - 254
19X-RAY DIFFRACTION19A255 - 270
20X-RAY DIFFRACTION20A271 - 284
21X-RAY DIFFRACTION21B48 - 60
22X-RAY DIFFRACTION22B61 - 79
23X-RAY DIFFRACTION23B80 - 94
24X-RAY DIFFRACTION24B95 - 106
25X-RAY DIFFRACTION25B107 - 118
26X-RAY DIFFRACTION26B119 - 125
27X-RAY DIFFRACTION27B126 - 136
28X-RAY DIFFRACTION28B137 - 145
29X-RAY DIFFRACTION29B146 - 159
30X-RAY DIFFRACTION30B160 - 168
31X-RAY DIFFRACTION31B169 - 186
32X-RAY DIFFRACTION32B187 - 199
33X-RAY DIFFRACTION33B200 - 205
34X-RAY DIFFRACTION34B206 - 214
35X-RAY DIFFRACTION35B215 - 232
36X-RAY DIFFRACTION36B233 - 246
37X-RAY DIFFRACTION37B247 - 260
38X-RAY DIFFRACTION38B261 - 267
39X-RAY DIFFRACTION39B268 - 278
40X-RAY DIFFRACTION40B279 - 285

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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