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- PDB-5dih: Structure of Haliangium ochraceum BMC-T HO-5812 -

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Basic information

Entry
Database: PDB / ID: 5dih
TitleStructure of Haliangium ochraceum BMC-T HO-5812
ComponentsMicrocompartments protein
KeywordsSTRUCTURAL 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 / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment protein trimer-1
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.444 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)131,5396
Polymers131,5396
Non-polymers00
Water5,963331
1
A: Microcompartments protein
C: Microcompartments protein
E: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)65,7703
Polymers65,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-36 kcal/mol
Surface area22980 Å2
MethodPISA
2
B: Microcompartments protein
D: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)65,7703
Polymers65,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-35 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.628, 66.378, 122.251
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Microcompartments protein


Mass: 21923.199 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 30 mM citric acid/70 mM BIS-Tris propane, 8% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→31.508 Å / Num. obs: 74297 / % possible obs: 96.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.3
Reflection shellResolution: 2.44→2.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.1 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FCH

3fch


Resolution: 2.444→31.508 Å / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 36.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 2022 5.63 %Random selection
Rwork0.2331 ---
obs0.2351 74297 91.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.444→31.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8687 0 0 331 9018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038804
X-RAY DIFFRACTIONf_angle_d0.59711937
X-RAY DIFFRACTIONf_dihedral_angle_d11.2943242
X-RAY DIFFRACTIONf_chiral_restr0.0341440
X-RAY DIFFRACTIONf_plane_restr0.0031548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4468-2.4890.38771740.34563158X-RAY DIFFRACTION79
2.489-2.53420.33551760.32093501X-RAY DIFFRACTION87
2.5342-2.58290.31362070.30843505X-RAY DIFFRACTION86
2.5829-2.63560.39761840.30093463X-RAY DIFFRACTION87
2.6356-2.69290.371970.31753442X-RAY DIFFRACTION85
2.6929-2.75550.4221760.2983397X-RAY DIFFRACTION84
2.7555-2.82430.31221730.28913411X-RAY DIFFRACTION84
2.8243-2.90060.33661940.27923606X-RAY DIFFRACTION89
2.9006-2.98590.32091940.26693537X-RAY DIFFRACTION89
2.9859-3.08210.31792060.26513604X-RAY DIFFRACTION89
3.0821-3.19210.29911870.24333608X-RAY DIFFRACTION89
3.1921-3.31970.27351760.24023641X-RAY DIFFRACTION89
3.3197-3.47060.29311950.23253527X-RAY DIFFRACTION88
3.4706-3.65320.24821840.22153595X-RAY DIFFRACTION89
3.6532-3.88150.25821800.23510X-RAY DIFFRACTION87
3.8815-4.18030.25381940.19253408X-RAY DIFFRACTION84
4.1803-4.59930.23061850.18113651X-RAY DIFFRACTION91
4.5993-5.2610.20282100.18013635X-RAY DIFFRACTION90
5.261-6.61370.24891950.23153656X-RAY DIFFRACTION91
6.6137-27.92880.26522130.19383591X-RAY DIFFRACTION89

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