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- PDB-4mpt: Crystal Structure of Periplasmic binding Protein Type 1 from Bord... -

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Basic information

Entry
Database: PDB / ID: 4mpt
TitleCrystal Structure of Periplasmic binding Protein Type 1 from Bordetella pertussis Tohama I
ComponentsPutative leu/ile/val-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / sulute-binding protein / alpha-beta structure
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Leu/ile/val-binding protein
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKim, Y. / Joachimiak, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Periplasmic binding Protein Type 1 from Bordetella pertussis Tohama I
Authors: Kim, Y. / Joachimiak, G. / Clancy, S. / Joachimiak, A.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative leu/ile/val-binding protein
B: Putative leu/ile/val-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6896
Polymers82,4862
Non-polymers2034
Water8,683482
1
A: Putative leu/ile/val-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3263
Polymers41,2431
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative leu/ile/val-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3633
Polymers41,2431
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.565, 86.565, 194.053
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Putative leu/ile/val-binding protein


Mass: 41242.852 Da / Num. of mol.: 2 / Fragment: delta-N21 / Mutation: residues 26-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Strain: Tohama I / Gene: BP0622 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7VS30
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 60 %(w/v) Tacsimate pH 7.0, 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 81351 / Num. obs: 81351 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 23.74 Å2 / Rsym value: 0.081 / Net I/σ(I): 10.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3435 / Rsym value: 0.549 / % possible all: 83.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1367)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→43.282 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.93 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.176 4073 5.01 %random
Rwork0.16 ---
all0.163 81296 --
obs0.163 81296 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 13 482 6133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075921
X-RAY DIFFRACTIONf_angle_d1.0938035
X-RAY DIFFRACTIONf_dihedral_angle_d15.1382222
X-RAY DIFFRACTIONf_chiral_restr0.07876
X-RAY DIFFRACTIONf_plane_restr0.0051084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7497-1.77980.22881710.23963248341979
1.7798-1.81220.25562120.23783541375386
1.8122-1.8470.21961910.22793876406793
1.847-1.88470.22581710.22073879405094
1.8847-1.92570.22892080.22273874408294
1.9257-1.97050.22991990.21513900409995
1.9705-2.01980.25451930.2043921411495
2.0198-2.07440.20531960.20243916411295
2.0744-2.13540.21482020.20293924412695
2.1354-2.20430.21052060.19823921412795
2.2043-2.28310.22561950.19343954414995
2.2831-2.37450.21671920.18963892408495
2.3745-2.48250.19322230.1823939416295
2.4825-2.61330.20272110.183894410595
2.6133-2.7770.19952290.17943924415394
2.777-2.99120.18952180.17783923414195
2.9912-3.2920.1622090.16363901411095
3.292-3.76770.14712220.13363944416695
3.7677-4.74450.11292240.09883901412595
4.7445-32.30240.16221950.12173947419294
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)
10.9739-0.0666-0.38811.05010.09341.04990.1127-0.15530.14380.2637-0.09750.0927-0.1362-0.0224-0.02070.2864-0.07350.07460.1982-0.02740.1442-24.78242.2349113.6666
21.66920.4162-0.09581.61360.31851.64630.0706-0.3111-0.20360.4721-0.0291-0.42380.10830.2236-0.01280.2728-0.0278-0.04930.2210.07050.2051-12.006825.9563114.9918
30.92790.491-0.65371.58910.46371.3098-0.1430.2281-0.3253-0.30820.1046-0.67760.11360.2214-0.00610.2379-0.02230.11850.2586-0.0380.382-6.460722.374796.8966
40.66270.069-0.24680.88060.16341.14210.0283-0.1277-0.12020.3228-0.14360.22680.1773-0.10270.10570.2886-0.07560.09070.20490.00420.1579-28.603926.8225113.3955
52.12290.0775-1.36083.1941-0.78933.66860.11020.305-0.0732-0.2301-0.0890.04110.1205-0.5743-0.08410.2796-0.0340.08670.26230.00820.2564-23.578115.032396.488
61.26590.0791-0.0141.2007-0.00630.8833-0.04990.3931-0.2699-0.10430.0299-0.15280.12420.08150.00180.1520.0034-0.0010.3282-0.09450.1739-19.049532.233472.6531
72.1311-0.4314-0.53761.49840.42671.15750.13920.39070.5515-0.2054-0.0443-0.0852-0.1979-0.0477-0.06090.18820.0026-0.01460.26220.06350.253-26.40354.458674.662
81.0116-0.0024-0.11221.11011.14241.19620.0776-0.18740.540.14140.0184-0.1314-0.14450.0266-0.04740.2363-0.0381-0.02520.2648-0.12960.3631-25.961960.207593.1539
90.9848-0.1022-0.36441.24370.23470.1677-0.0773-0.09430.04080.12920.03280.03110.0008-0.10390.03970.1861-0.0022-0.03960.2857-0.0670.1991-35.120943.325786.8695
100.6357-0.1468-0.07360.8750.3230.9971-0.01310.4816-0.1391-0.1993-0.05720.1797-0.0267-0.19470.03950.16860.0067-0.05770.4303-0.07690.1499-32.668336.510269.5373
112.60660.0389-0.72282.011-0.15444.54610.185-0.0566-0.04260.22970.09490.28140.3348-0.0566-0.18210.22890.0347-0.05770.2323-0.06040.228-42.063347.158489.4118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 250 )
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 354 )
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 375 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 191 )
8X-RAY DIFFRACTION8chain 'B' and (resid 192 through 224 )
9X-RAY DIFFRACTION9chain 'B' and (resid 225 through 280 )
10X-RAY DIFFRACTION10chain 'B' and (resid 281 through 354 )
11X-RAY DIFFRACTION11chain 'B' and (resid 355 through 375 )

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