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- PDB-5dii: Structure of an engineered bacterial microcompartment shell prote... -

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Basic information

Entry
Database: PDB / ID: 5dii
TitleStructure of an engineered bacterial microcompartment shell protein binding a [4Fe-4S] cluster
ComponentsMicrocompartments protein
KeywordsSTRUCTURAL PROTEIN / Engineered Protein / Bacterial Microcompartments
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits ...Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Bacterial microcompartment protein trimer-1
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsSutter, M. / Aussignargues, C. / Turmo, A. / Kerfeld, C.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster.
Authors: Aussignargues, C. / Pandelia, M.E. / Sutter, M. / Plegaria, J.S. / Zarzycki, J. / Turmo, A. / Huang, J. / Ducat, D.C. / Hegg, E.L. / Gibney, B.R. / Kerfeld, C.A.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 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_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,3398
Polymers131,6366
Non-polymers7032
Water7,332407
1
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1694
Polymers65,8183
Non-polymers3521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-61 kcal/mol
Surface area22130 Å2
MethodPISA
2
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1694
Polymers65,8183
Non-polymers3521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-59 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.897, 55.558, 117.930
Angle α, β, γ (deg.)83.45, 81.22, 86.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Microcompartments protein


Mass: 21939.266 Da / Num. of mol.: 6 / Mutation: S55C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5812 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LHE3
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 250mM Na acetate trihydrate, 100mM Tris pH 8.5, 26% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.8→38.625 Å / Num. obs: 176094 / % possible obs: 96.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.4 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIH

5dih


Resolution: 1.804→38.625 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1989 2.1 %Random selection
Rwork0.1879 ---
obs0.1886 176084 89.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.804→38.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8812 0 16 407 9235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018971
X-RAY DIFFRACTIONf_angle_d1.40112183
X-RAY DIFFRACTIONf_dihedral_angle_d12.4313297
X-RAY DIFFRACTIONf_chiral_restr0.051458
X-RAY DIFFRACTIONf_plane_restr0.0061583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8039-1.82770.38981250.38875056X-RAY DIFFRACTION70
1.8277-1.85270.36061370.36846574X-RAY DIFFRACTION86
1.8527-1.87920.36991320.34896391X-RAY DIFFRACTION87
1.8792-1.90720.30221330.32086471X-RAY DIFFRACTION87
1.9072-1.9370.37691560.30596470X-RAY DIFFRACTION87
1.937-1.96880.29311150.29536496X-RAY DIFFRACTION88
1.9688-2.00270.29911600.27586475X-RAY DIFFRACTION88
2.0027-2.03910.28671360.25996632X-RAY DIFFRACTION89
2.0391-2.07830.32761120.2366525X-RAY DIFFRACTION88
2.0783-2.12080.26761740.22076530X-RAY DIFFRACTION88
2.1208-2.16690.23971260.21186593X-RAY DIFFRACTION89
2.1669-2.21730.22371480.2046646X-RAY DIFFRACTION89
2.2173-2.27270.24341420.19356669X-RAY DIFFRACTION90
2.2727-2.33420.23141360.19166589X-RAY DIFFRACTION89
2.3342-2.40280.20911590.1876730X-RAY DIFFRACTION90
2.4028-2.48040.20131340.17946672X-RAY DIFFRACTION91
2.4804-2.5690.24961680.18556711X-RAY DIFFRACTION91
2.569-2.67180.24431370.18146841X-RAY DIFFRACTION91
2.6718-2.79340.19661250.1616703X-RAY DIFFRACTION91
2.7934-2.94060.21881460.16386847X-RAY DIFFRACTION92
2.9406-3.12480.24931440.16566887X-RAY DIFFRACTION92
3.1248-3.36590.22881540.15716861X-RAY DIFFRACTION93
3.3659-3.70440.18441450.15836917X-RAY DIFFRACTION93
3.7044-4.23990.14651460.1396947X-RAY DIFFRACTION93
4.2399-5.33960.15891510.14736907X-RAY DIFFRACTION94
5.3396-38.63360.17831590.17157244X-RAY DIFFRACTION98

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