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- PDB-3dzm: Crystal structure of a major outer membrane protein from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 3dzm
TitleCrystal structure of a major outer membrane protein from Thermus thermophilus HB27
ComponentsHypothetical conserved protein
KeywordsUNKNOWN FUNCTION / OMP / Thermus thermophilus HB27 / beta-barrel / TtoA
Function / homologyouter membrane protein from Thermus thermophilus HB27. / Porin / Beta Barrel / Mainly Beta / metal ion binding / Hypothetical conserved protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.801 Å
AuthorsBrosig, A. / Diederichs, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of a major outer membrane protein from Thermus thermophilus HB27
Authors: Brosig, A. / Nesper, J. / Boos, W. / Welte, W. / Diederichs, K.
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical conserved protein
B: Hypothetical conserved protein
C: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,69312
Polymers68,7343
Non-polymers1,9599
Water73941
1
A: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5644
Polymers22,9111
Non-polymers6533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5644
Polymers22,9111
Non-polymers6533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5644
Polymers22,9111
Non-polymers6533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Hypothetical conserved protein
B: Hypothetical conserved protein
C: Hypothetical conserved protein
hetero molecules

A: Hypothetical conserved protein
B: Hypothetical conserved protein
C: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,38624
Polymers137,4686
Non-polymers3,91818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area16860 Å2
ΔGint-181 kcal/mol
Surface area57580 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-79 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.980, 166.980, 98.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical conserved protein / TtoA


Mass: 22911.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C0834 / Plasmid: pMK18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: Q72JD8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.74578.59008
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop90.2M sodium malonate, 44% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop90.2M sodium malonate, 43% MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.072
SYNCHROTRONSLS X06SA20.9252
SYNCHROTRONSLS X06SA31.0162
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 1, 2008mirrors
PSI PILATUS 6M2PIXELApr 9, 2008mirrors
PSI PILATUS 6M3PIXELMay 5, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
3Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0721
20.92521
31.01621
ReflectionResolution: 2.8→40 Å / Num. all: 38811 / Num. obs: 38811 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 86.43 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 1.42 / Num. unique all: 6196 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.801→37.126 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.38 / Isotropic thermal model: Isotropic and TLS / σ(F): 2 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1946 5.01 %5% of reflections, selected randomly
Rwork0.196 36864 --
obs0.198 38810 99.53 %-
all-38810 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.134 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 342.47 Å2 / Biso mean: 100.676 Å2 / Biso min: 48.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.925 Å20 Å20 Å2
2--0.925 Å20 Å2
3----1.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.409 Å
Refinement stepCycle: LAST / Resolution: 2.801→37.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4626 0 129 41 4796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134863
X-RAY DIFFRACTIONf_angle_d1.6496554
X-RAY DIFFRACTIONf_chiral_restr0.102681
X-RAY DIFFRACTIONf_plane_restr0.007854
X-RAY DIFFRACTIONf_dihedral_angle_d20.8921723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.801-2.8710.3391340.3032397253193
2.871-2.9490.3381230.25826432766100
2.949-3.0360.2661430.23526282771100
3.036-3.1340.2331560.20525922748100
3.134-3.2460.211210.17926362757100
3.246-3.3750.2181330.15126432776100
3.375-3.5290.1921390.16226422781100
3.529-3.7150.2051470.16726252772100
3.715-3.9470.2081350.17626312766100
3.947-4.2520.211660.16426222788100
4.252-4.6790.2151330.15526632796100
4.679-5.3540.1821340.1726752809100
5.354-6.7390.281390.23426842823100
6.739-37.1290.2571430.21427832926100
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)
10.79361.9661.25245.12221.58641.1810.18590.00720.0813-0.19290.2111-1.3948-0.20230.485-0.33810.5591-0.034-0.010.6271-0.04560.707163.7232-59.4799-23.3923
23.48171.54250.64561.63481.70032.04490.10260.1091-0.56450.14260.02820.05670.19210.1906-0.18070.50690.0522-0.03130.6007-0.02090.58361.6383-67.4399-24.0335
34.25721.6811.72443.797-0.47064.48660.2262-0.2941-0.34850.9105-0.2249-0.2440.5221-0.2447-0.07420.8651-0.1188-0.05240.47210.06890.564383.6723-33.7948-29.3897
42.20140.7789-0.55493.2914-1.76672.532-0.1341-0.20680.13420.75560.0404-0.1196-0.42690.29980.14170.75750.0018-0.02190.43450.02490.456988.1664-28.4227-27.7147
50.98951.47463.47431.79971.30553.5917-0.4196-0.04460.5118-0.3916-0.00530.4889-0.5049-0.86270.55120.68070.0106-0.12230.7536-0.14090.835838.2063-50.541-22.8242
61.17250.59872.34681.9259-0.27382.3867-0.3808-0.51440.49750.03560.2230.4006-0.37280.01940.20890.49520.0325-0.04430.6487-0.22040.777838.6693-49.2987-16.309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:93)
2X-RAY DIFFRACTION2(chain A and resid 94:207)
3X-RAY DIFFRACTION3(chain B and resid 1:93)
4X-RAY DIFFRACTION4(chain B and resid 94:207)
5X-RAY DIFFRACTION5(chain C and resid 1:92)
6X-RAY DIFFRACTION6(chain C and resid 93:207)

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