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- PDB-3u27: Crystal structure of ethanolamine utilization protein EutL from L... -

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Basic information

Entry
Database: PDB / ID: 3u27
TitleCrystal structure of ethanolamine utilization protein EutL from Leptotrichia buccalis C-1013-b
ComponentsMicrocompartments proteinBacterial microcompartment
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / PSI-Biology / MCSG / ALPHA-BETA-ALPHA fold / bacterial Microcompartment / SHELL PROTEIN / ETHANOLAMINE / Midwest Center for Structural Genomics
Function / homology
Function and homology information


bacterial microcompartment / structural molecule activity / metal ion binding
Similarity search - Function
Bacterial microcompartment shell protein EutL / Bacterial microcompartment shell protein, EutL/PduB type / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Microcompartments protein
Similarity search - Component
Biological speciesLeptotrichia buccalis C-1013-b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 Å
AuthorsWu, R. / Gu, M. / Kerfeld, C.A. / Salmeen, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ethanolamine utilization protein EutL from Leptotrichia buccalis C-1013-b
Authors: Wu, R. / Gu, M. / Kerfeld, C.A. / Salmeen, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Apr 11, 2012Group: Database references / Structure summary
Revision 1.3Sep 12, 2012Group: Database references / Structure summary
Revision 1.4Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3] / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Microcompartments protein
A: Microcompartments protein
B: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,19322
Polymers138,1356
Non-polymers1,05816
Water21,0961171
1
C: Microcompartments protein
B: Microcompartments protein
hetero molecules

E: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)69,47010
Polymers69,0673
Non-polymers4027
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area9730 Å2
ΔGint-82 kcal/mol
Surface area22750 Å2
MethodPISA
2
A: Microcompartments protein
D: Microcompartments protein
F: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,72312
Polymers69,0673
Non-polymers6569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-89 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.854, 105.644, 101.551
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Microcompartments protein / Bacterial microcompartment


Mass: 23022.420 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia buccalis C-1013-b (bacteria)
Strain: DSM 1135 / Gene: Lebu_0063 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: C7NCS6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1171 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4M Na Nitrate, 0.1M BistrisPropane 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 10, 2011 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→42 Å / Num. all: 179843 / Num. obs: 176454 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.41 Å2 / Rsym value: 0.1 / Net I/σ(I): 14.58
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.28 / Rsym value: 0.667 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.852→34.417 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 8839 5.01 %
Rwork0.1572 --
obs0.1584 176432 97.6 %
all-176440 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.032 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1602 Å20 Å20.6177 Å2
2--5.6833 Å20 Å2
3----5.8435 Å2
Refinement stepCycle: LAST / Resolution: 1.852→34.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9539 0 61 1171 10771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079886
X-RAY DIFFRACTIONf_angle_d1.08913447
X-RAY DIFFRACTIONf_dihedral_angle_d12.6713527
X-RAY DIFFRACTIONf_chiral_restr0.0781554
X-RAY DIFFRACTIONf_plane_restr0.0051769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8517-1.87280.26342690.25045306X-RAY DIFFRACTION93
1.8728-1.89480.2832820.24215507X-RAY DIFFRACTION97
1.8948-1.91790.2423330.21565538X-RAY DIFFRACTION97
1.9179-1.94220.25342920.21475550X-RAY DIFFRACTION98
1.9422-1.96770.22373130.19455574X-RAY DIFFRACTION98
1.9677-1.99470.19383100.17165623X-RAY DIFFRACTION98
1.9947-2.02320.1993110.16245562X-RAY DIFFRACTION98
2.0232-2.05340.21172860.15975585X-RAY DIFFRACTION98
2.0534-2.08540.17912990.15985587X-RAY DIFFRACTION98
2.0854-2.11960.19052920.15545656X-RAY DIFFRACTION98
2.1196-2.15620.17852880.15835598X-RAY DIFFRACTION98
2.1562-2.19540.1962960.15725602X-RAY DIFFRACTION98
2.1954-2.23760.17422930.14995609X-RAY DIFFRACTION98
2.2376-2.28330.18162920.14745642X-RAY DIFFRACTION99
2.2833-2.33290.17772910.14785673X-RAY DIFFRACTION99
2.3329-2.38710.18962960.15635709X-RAY DIFFRACTION100
2.3871-2.44680.19482870.15765681X-RAY DIFFRACTION100
2.4468-2.5130.17993320.15285674X-RAY DIFFRACTION99
2.513-2.58690.19322980.1525668X-RAY DIFFRACTION99
2.5869-2.67040.18263140.15685647X-RAY DIFFRACTION99
2.6704-2.76580.18743110.15675648X-RAY DIFFRACTION99
2.7658-2.87640.18693000.15475666X-RAY DIFFRACTION99
2.8764-3.00730.1763070.14725602X-RAY DIFFRACTION98
3.0073-3.16570.16913020.15455564X-RAY DIFFRACTION97
3.1657-3.36390.16812670.15185558X-RAY DIFFRACTION97
3.3639-3.62340.19162720.14925546X-RAY DIFFRACTION96
3.6234-3.98750.15752790.13965516X-RAY DIFFRACTION96
3.9875-4.56340.14662830.12965498X-RAY DIFFRACTION95
4.5634-5.74510.1492730.13925476X-RAY DIFFRACTION95
5.7451-34.42320.19272710.19525528X-RAY DIFFRACTION94
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)
10.50690.0177-0.15310.5353-0.34830.86940.0167-0.0264-0.0169-0.0644-0.0372-0.02510.07710.1228-00.12560.00910.00990.1296-0.00320.124222.240212.2445-28.7537
21.036-0.41440.52320.6671-0.2710.46060.03180.0206-0.1127-0.01790.03190.03610.04750.04820.00140.11910.01620.00770.11570.00230.130952.7797-17.832531.6495
30.5154-0.00240.18210.64360.33570.85780.0082-0.01130.0095-0.0524-0.03560.0086-0.0799-0.1211-0.00080.05830.0094-0.00340.06460.00520.053428.19110.232822.1095
41.0241-0.3644-0.43720.60360.18470.48650.04660.00850.1285-0.01830.034-0.0269-0.0569-0.05590.00350.1270.0171-0.00360.1188-0.00570.1399-2.166530.2662-19.3703
50.551-0.4212-0.29150.78720.39680.4882-0.0571-0.15050.08330.08350.0985-0.0774-0.00060.06360.010.12580.0101-0.00550.1545-0.03960.118945.24368.2014-53.6502
60.551-0.50790.3920.8383-0.36890.5668-0.0661-0.1345-0.07760.08730.09490.0780.0118-0.05620.00260.13470.00570.00920.15520.04030.13385.54184.0673-2.8749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A resid 1:217A0
2X-RAY DIFFRACTION2chain B resid 1:217B0
3X-RAY DIFFRACTION3chain C resid 1:217C0
4X-RAY DIFFRACTION4chain D resid 1:217D0
5X-RAY DIFFRACTION5chain E resid 1:217E0
6X-RAY DIFFRACTION6chain F resid 1:217F0

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