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- PDB-4tlh: Monoclinic Crystal Structure of EutL from Clostridium Perfringens -

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Basic information

Entry
Database: PDB / ID: 4tlh
TitleMonoclinic Crystal Structure of EutL from Clostridium Perfringens
ComponentsEthanolamine utilization protein EutL
KeywordsTRANSPORT PROTEIN / bacterial microcompartment / Eut / BMC shell protein / ethanolamine / microcrystallography / structural polymorphism
Function / homology
Function and homology information


bacterial microcompartment / cobalamin binding / structural molecule activity / metal ion binding
Similarity search - Function
Bacterial microcompartment shell protein EutL / Bacterial microcompartment shell protein, EutL/PduB type / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
Ethanolamine utilization protein EutL / Bacterial microcompartment shell protein EutL
Similarity search - Component
Biological speciesClostridium perfringens E str. JGS1987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
Model detailsbacterial microcompartments (BMC) superfamily
AuthorsThompson, M.C. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2018
Title: Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism
Authors: Thompson, M.C. / Cascio, D. / Yeates, T.O.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethanolamine utilization protein EutL
B: Ethanolamine utilization protein EutL
C: Ethanolamine utilization protein EutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2326
Polymers71,1503
Non-polymers813
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-104 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.440, 66.030, 79.380
Angle α, β, γ (deg.)90.000, 108.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-348-

HOH

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Components

#1: Protein Ethanolamine utilization protein EutL


Mass: 23716.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens E str. JGS1987 (bacteria)
Gene: eutL, AC3_1081 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: B1BQ33, UniProt: Q8XLZ0*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M sodium potassium phosphate, 0.25 sodium chloride, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→33.427 Å / Num. obs: 63757 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 16.86 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.11 / Χ2: 0.991 / Net I/σ(I): 11.02 / Num. measured all: 235518
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.740.6350.9931.6217332471446921.15999.5
1.74-1.790.7060.7782.0216965459245850.90899.8
1.79-1.840.8120.6032.616611448844750.70399.7
1.84-1.90.8730.4763.2316132434443320.55599.7
1.9-1.960.9340.3434.4115450417441570.499.6
1.96-2.030.9550.2635.6515223409740850.30699.7
2.03-2.110.9720.2037.1414623393339160.23799.6
2.11-2.190.9810.168.5214070379337740.18799.5
2.19-2.290.9840.1459.4113391360535880.16999.5
2.29-2.40.9880.11910.9313107352335070.13999.5
2.4-2.530.9910.10112.3112215328232750.11899.8
2.53-2.690.9940.07914.8911559312831140.09399.6
2.69-2.870.9950.06917.0310995297329630.08199.7
2.87-3.10.9950.05819.889967272327110.06899.6
3.1-3.40.9960.048239146254925280.05799.2
3.4-3.80.9970.04126.998095229422680.04998.9
3.8-4.390.9970.03628.826900202819970.04398.5
4.39-5.380.9980.03131.416224172717020.03698.6
5.38-7.60.9980.03229.974898135513440.03899.2
7.60.9990.02633.6326157667440.03197.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.18 Å37.69 Å
Translation7.18 Å37.69 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1555)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.427 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 1999 3.14 %
Rwork0.1634 61738 -
obs0.1644 63737 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.54 Å2 / Biso mean: 24.1918 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 1.7→33.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 3 504 5272
Biso mean--22.22 33.46 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094967
X-RAY DIFFRACTIONf_angle_d1.156781
X-RAY DIFFRACTIONf_chiral_restr0.046799
X-RAY DIFFRACTIONf_plane_restr0.006897
X-RAY DIFFRACTIONf_dihedral_angle_d12.3871782
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 (%)
1.7-1.74250.32271410.30784382452399
1.7425-1.78960.28871430.274744064549100
1.7896-1.84230.30081420.25143924534100
1.8423-1.90180.27641420.226643884530100
1.9018-1.96970.2261410.188643524493100
1.9697-2.04860.20451440.169844244568100
2.0486-2.14180.17851430.163644154558100
2.1418-2.25470.21821420.155743844526100
2.2547-2.39590.22431430.161444194562100
2.3959-2.58080.23271430.163744074550100
2.5808-2.84040.19611430.152444114554100
2.8404-3.25120.18081420.15244354577100
3.2512-4.09490.15911440.13384418456299
4.0949-33.43310.13811460.1344505465199
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)
11.18480.6663-0.21361.49680.23581.00930.05120.01720.15240.0818-0.05180.2190.0359-0.1111-0.00110.1080.01290.01950.10850.0050.1996101.30623.444195.4039
20.8321-0.37780.03381.50620.05540.3235-0.0295-0.00640.0303-0.01840.0455-0.1082-0.01660.0182-0.01950.1111-0.00560.0250.1096-0.00210.1714132.39420.988895.6437
31.5339-0.08610.20360.8082-0.07620.3253-0.00820.0149-0.1566-0.0394-0.00360.04720.05050.00570.0050.1364-0.00340.02450.092-0.01980.1675114.5511-25.434792.4324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 220
2X-RAY DIFFRACTION2chain BB1 - 217
3X-RAY DIFFRACTION3chain CC1 - 216

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