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- PDB-3pam: Crystal structure of a domain of transmembrane protein of ABC-typ... -

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Basic information

Entry
Database: PDB / ID: 3pam
TitleCrystal structure of a domain of transmembrane protein of ABC-type oligopeptide transport system from Bartonella henselae str. Houston-1
ComponentsTransmembrane protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Bacterial extracellular solute-binding proteins / family 5 Middle / PSI2
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space
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
ETHANOL / Transmembrane protein / Transmembrane protein
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsNocek, B. / Stein, A. / Mack, J. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a domain of transmembrane protein of ABC-type oligopeptide transport system from Bartonella henselae str. Houston-1"
Authors: Nocek, B. / Stein, A. / Mack, J. / Buck, K. / Joachimiak, A.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 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: Transmembrane protein
B: Transmembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,59112
Polymers59,1312
Non-polymers46110
Water1,20767
1
A: Transmembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8427
Polymers29,5651
Non-polymers2766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transmembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7505
Polymers29,5651
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.847, 39.715, 101.353
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Transmembrane protein


Mass: 29565.344 Da / Num. of mol.: 2 / Fragment: sequence database residues 319-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: BH08740 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q6G3A9, UniProt: A0A0H3LXD4*PLUS
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17 % PEG 4000, 8.5% 2-Propanol, Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 315r / Detector: CCD / Date: Jul 28, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.876
11-L, K, H20.124
ReflectionResolution: 2.31→37 Å / Num. all: 32185 / Num. obs: 31961 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19
Reflection shellResolution: 2.31→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.53 / Num. unique all: 3201 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.31→36.95 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.715 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.061 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25684 1616 5.1 %RANDOM
Rwork0.22331 ---
all0.23 31871 --
obs0.22496 30255 88.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.452 Å2
Baniso -1Baniso -2Baniso -3
1--4.46 Å20 Å2-4.56 Å2
2---6.84 Å20 Å2
3---11.3 Å2
Refinement stepCycle: LAST / Resolution: 2.31→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 30 67 3980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9415408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04924.162185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.61615615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4171523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213071
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_it0.4051.52528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70524011
X-RAY DIFFRACTIONr_scbond_it1.43131465
X-RAY DIFFRACTIONr_scangle_it2.0414.51396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.366 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0 0
Rwork0 0
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)
13.8662-1.1488-4.53052.78292.12641.6233-0.3596-0.4495-1.64780.138-0.01770.92360.8120.00640.37730.6726-0.1523-0.05640.47680.22990.956216.2741-5.80550.2791
25.2576-2.4687-4.68685.4085-0.87665.8017-0.028-0.05520.2841-0.24720.02880.0478-0.30240.0726-0.00080.3726-0.0314-0.07630.260.04860.297220.70157.795144.7731
36.5748-1.96581.72977.5917-2.83265.57810.11480.1823-0.5678-0.7023-0.0610.03840.59050.2944-0.05380.35270.0140.07820.351-0.05310.275923.3322-3.738539.5336
4-1.23-1.4781-7.316.5362-3.2766-13.31930.1861-0.6314-1.31920.43390.0092-0.40440.69540.3026-0.19530.94760.061-0.21140.80970.38490.997627.316-16.764446.0074
55.4274-1.16853.1880.3219-0.6652.68940.3271-0.0303-1.04510.1816-0.0846-0.04840.64350.3285-0.24250.6062-0.0046-0.01910.41780.07720.654713.353-14.159545.3911
60.81390.56341.1118-0.21560.97022.2455-0.11360.4462-0.3772-0.3538-0.0563-0.0024-0.0948-0.10680.16990.4217-0.080.08710.5762-0.04560.4432.1651-0.625431.6583
710.07694.75-4.575225.9587-6.64645.1626-0.38610.83060.3306-0.66220.54940.6055-0.0146-0.5017-0.16330.6533-0.10180.02170.6121-0.09240.39059.0335-6.157429.3735
81.90193.6588-3.68587.8197-0.10013.0528-0.084-0.4037-0.45080.34690.0232-1.02790.50490.89390.06090.62680.07180.02170.5958-0.05260.469625.3466-11.716535.4937
92.6401-6.2182-2.74316.9558-4.70197.5983-0.03220.501-0.1031-0.94150.14220.38490.0311-0.3127-0.10990.3678-0.15830.08140.50450.00440.271227.99882.094931.805
101.04593.3719-1.12143.813-1.98337.2065-0.12970.01730.50070.12490.05510.4067-0.8147-0.43440.07470.3768-0.001-0.0070.34370.00240.32335.21378.630338.4211
113.03-1.2751-1.635210.9535-8.025111.9111-0.2749-0.7035-0.51460.82830.1113-0.0529-0.1894-0.19620.16370.3034-0.03470.05040.51580.1290.34326.7583-2.71755.7456
124.8218-4.50486.4446.208-0.18383.30390.5238-0.6608-0.4699-0.2143-0.03530.20421.0755-0.3839-0.48840.43460.05590.07280.31240.12830.307729.1939-8.117951.003
138.1721-2.9546-3.28926.3741-4.16258.3088-0.0043-0.2701-0.1473-0.21980.2004-0.43770.4370.4245-0.19610.2714-0.00350.05820.36420.03880.383133.7717-1.720844.9604
144.4435-3.6666-0.05243.96661.90511.8761-0.1219-0.59690.1450.3120.1972-0.0828-0.04080.0618-0.07530.4176-0.0070.08680.59520.04760.343522.87462.372961.9965
1535.5535-6.0181-6.83674.734-7.834311.3828-0.1517-0.56330.42650.3536-0.0162-0.1069-0.6031-0.04040.16790.2638-0.0045-0.00140.3019-0.01070.272120.25516.984754.6431
1613.95745.5815-0.40421.80050.6716-0.5630.01180.0241-0.1329-0.0357-0.06110.33680.3051-0.23450.04920.4179-0.05120.05650.6210.0630.593110.378-5.941253.7999
175.31491.19681.26313.10110.40874.03-0.0978-0.14220.184-0.01770.0420.2523-0.1019-0.30240.05580.25830.02130.05420.25760.01450.28916.4045.362849.7897
1812.011310.59941.20789.222-0.26892.29580.05110.1710.0521-0.1054-0.00460.2794-0.1486-0.3954-0.04660.35750.02280.02120.3813-0.01290.3701-6.6379-0.003443.0695
194.0566-0.1336-1.53360.12710.3227-0.0328-0.04740.7932-0.2989-0.17160.06250.1712-0.0539-0.2842-0.01510.3755-0.05730.03230.4058-0.00530.42460.9447-4.507539.2037
203.1838-1.28732.28070.15-0.51392.43180.1758-0.5166-0.8185-0.17570.16480.29590.7268-0.3761-0.34060.4287-0.00340.07790.39930.03090.456215.6563-7.345445.9921
212.30382.3599-3.6109-2.312-1.790816.97940.2231-0.2164-0.7045-0.0715-0.5003-0.40182.14121.12230.27710.8903-0.0827-0.2280.46440.18340.652545.5411-16.60882.0144
2210.7496-0.10126.2831-1.24651.77153.9605-0.21510.6130.9671-0.358-0.1887-0.0567-0.6125-0.10180.40390.4910.04470.10860.42510.08840.335345.0069-1.751979.2839
23-1.0142-2.1983-7.59749.3075.62464.42610.9144-0.78050.4658-0.1698-0.49560.191-0.3635-0.641-0.41880.4481-0.01120.30361.0131-0.01310.389235.724-5.951478.7327
241.5922-6.6926-1.074312.80781.77031.34460.09670.3435-0.5833-0.1377-0.19660.90850.3859-0.78770.09990.5216-0.13440.06830.6660.04230.381338.6206-20.030771.8105
251.6262-0.2032-1.88811.64251.20382.37660.060.1075-0.0095-0.13370.2915-0.30130.33970.1754-0.35140.7612-0.0415-0.00960.40240.02920.479843.4242-27.706475.7612
26-0.63524.1663.27844.16554.72559.980.34080.0285-0.6439-0.0680.16570.56380.3732-0.8553-0.50650.6898-0.15530.07650.69390.22250.741232.9945-22.482295.0706
273.73051.67360.28183.80432.64633.3719-0.02580.1901-0.1733-0.24580.1850.25880.09-1.1067-0.15930.6386-0.06690.12941.03010.27870.355127.4365-10.201494.9415
282.604-3.80133.39554.3628-3.52536.23550.28640.0342-0.6133-0.3059-0.05621.3425-0.31610.1417-0.23020.6824-0.43580.02441.06930.09370.863128.8088-20.094280.349
2912.2154.02225.06514.93052.93736.9550.032-0.0339-0.0144-0.85810.11971.3957-0.0861-0.6537-0.15170.47870.01970.02390.84410.08380.42229.6126-8.00670.4146
307.3345-0.75091.81331.0731-1.50382.1336-0.1056-0.47520.5071-0.0330.14080.2575-0.4664-0.3397-0.03520.59750.06470.04070.4920.07650.311937.5464-0.585364.3377
3111.2724-9.23121.50247.7141-1.81964.12950.06370.1035-0.09740.3151-0.0871-0.0590.27090.69180.02350.41910.01960.03910.4291-0.0350.22853.537-14.24673.2756
325.006-2.0075-5.18285.11571.82457.85680.0782-0.0197-0.11830.1210.0327-0.18190.56910.3047-0.1110.54950.0390.00820.3715-0.0230.211948.3711-17.868769.0737
331.8447-5.70124.15884.3611-4.75776.40140.01390.1928-0.219-0.11970.17860.1075-0.0507-0.3328-0.19250.35880.03080.12190.50650.02280.261343.0472-10.892565.6241
347.41842.21650.99188.23371.8186.4679-0.0027-0.09940.54440.2530.0918-0.5797-0.30620.535-0.08910.39860.03960.06910.4611-0.02510.211960.0763-9.747377.6686
353.6235-7.3959-2.929213.823-3.321225.64810.2133-0.4520.5490.33090.0683-0.8534-0.96250.7308-0.28160.4225-0.01050.12830.38660.02830.200352.2447-4.990279.8522
36-0.2622-0.0442-0.3632-1.34961.0508-2.9782-0.0366-0.1938-0.39890.2380.0888-0.09660.3479-0.2519-0.05220.75530.02670.0360.59430.06440.590548.2224-18.659291.5571
374.14741.1058-0.76964.41731.00323.98370.1055-0.54720.11860.34580.1052-0.2695-0.34760.2817-0.21070.46970.01570.0910.3937-0.01320.241248.922-6.903493.1376
380.357-0.55522.812.4593-1.36856.0922-0.035-0.18360.17410.30520.32840.4788-0.5387-1.005-0.29330.47270.08660.19190.42090.11050.343740.6723-6.232693.195
393.94271.5428-1.58211.1874-1.68723.04620.2116-0.47470.05370.52770.14840.0066-0.1235-0.2806-0.360.65740.05760.10540.51240.0590.259538.0685-15.0171106.9402
400.9366-0.2589-0.98781.257-0.37972.32540.0240.0051-0.30950.15260.14770.25970.2524-0.289-0.17170.462-0.06510.03890.47160.09990.333238.3068-17.790689.877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A319 - 324
2X-RAY DIFFRACTION2A325 - 335
3X-RAY DIFFRACTION3A336 - 347
4X-RAY DIFFRACTION4A348 - 352
5X-RAY DIFFRACTION5A353 - 374
6X-RAY DIFFRACTION6A375 - 394
7X-RAY DIFFRACTION7A395 - 400
8X-RAY DIFFRACTION8A401 - 417
9X-RAY DIFFRACTION9A418 - 429
10X-RAY DIFFRACTION10A430 - 444
11X-RAY DIFFRACTION11A445 - 456
12X-RAY DIFFRACTION12A457 - 462
13X-RAY DIFFRACTION13A463 - 474
14X-RAY DIFFRACTION14A475 - 488
15X-RAY DIFFRACTION15A489 - 494
16X-RAY DIFFRACTION16A495 - 503
17X-RAY DIFFRACTION17A504 - 535
18X-RAY DIFFRACTION18A536 - 547
19X-RAY DIFFRACTION19A548 - 562
20X-RAY DIFFRACTION20A563 - 574
21X-RAY DIFFRACTION21B319 - 325
22X-RAY DIFFRACTION22B326 - 331
23X-RAY DIFFRACTION23B332 - 339
24X-RAY DIFFRACTION24B340 - 349
25X-RAY DIFFRACTION25B350 - 365
26X-RAY DIFFRACTION26B366 - 380
27X-RAY DIFFRACTION27B381 - 396
28X-RAY DIFFRACTION28B397 - 415
29X-RAY DIFFRACTION29B416 - 429
30X-RAY DIFFRACTION30B430 - 445
31X-RAY DIFFRACTION31B446 - 454
32X-RAY DIFFRACTION32B455 - 464
33X-RAY DIFFRACTION33B465 - 475
34X-RAY DIFFRACTION34B476 - 488
35X-RAY DIFFRACTION35B489 - 494
36X-RAY DIFFRACTION36B495 - 506
37X-RAY DIFFRACTION37B507 - 525
38X-RAY DIFFRACTION38B526 - 538
39X-RAY DIFFRACTION39B539 - 548
40X-RAY DIFFRACTION40B549 - 574

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