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- PDB-5djb: Structure of the Haliangium ochraceum BMC-H shell protein -

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Basic information

Entry
Database: PDB / ID: 5djb
TitleStructure of the Haliangium ochraceum BMC-H shell protein
ComponentsMicrocompartments proteinBacterial microcompartment
KeywordsSTRUCTURAL PROTEIN / Bacterial Microcompartments
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits ...BMC (bacterial microcompartment) domain / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / 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 homohexamer
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsSutter, M. / Kerfeld, C.A.
CitationJournal: Nano Lett. / Year: 2016
Title: Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy.
Authors: Sutter, M. / Faulkner, M. / Aussignargues, C. / Paasch, B.C. / Barrett, S. / Kerfeld, C.A. / Liu, L.N.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 23, 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

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
G: Microcompartments protein
H: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)81,0148
Polymers81,0148
Non-polymers00
Water17,853991
1
A: Microcompartments protein
B: Microcompartments protein

A: Microcompartments protein
B: Microcompartments protein

A: Microcompartments protein
B: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)60,7606
Polymers60,7606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Buried area11020 Å2
ΔGint-81 kcal/mol
Surface area23400 Å2
MethodPISA
2
C: Microcompartments protein
D: Microcompartments protein

C: Microcompartments protein
D: Microcompartments protein

C: Microcompartments protein
D: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)60,7606
Polymers60,7606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area11050 Å2
ΔGint-81 kcal/mol
Surface area23050 Å2
MethodPISA
3
E: Microcompartments protein
F: Microcompartments protein

E: Microcompartments protein
F: Microcompartments protein

E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)60,7606
Polymers60,7606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area10820 Å2
ΔGint-80 kcal/mol
Surface area20860 Å2
MethodPISA
4
G: Microcompartments protein
H: Microcompartments protein

G: Microcompartments protein
H: Microcompartments protein

G: Microcompartments protein
H: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)60,7606
Polymers60,7606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Buried area10830 Å2
ΔGint-78 kcal/mol
Surface area20930 Å2
MethodPISA
5
A: Microcompartments protein
B: Microcompartments protein

A: Microcompartments protein
B: Microcompartments protein

A: Microcompartments protein
B: Microcompartments protein

G: Microcompartments protein
H: Microcompartments protein

G: Microcompartments protein
H: Microcompartments protein

G: Microcompartments protein
H: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)121,52112
Polymers121,52112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_866-y+3,x-y+1,z+11
crystal symmetry operation3_786-x+y+2,-x+3,z+11
Buried area29490 Å2
ΔGint-225 kcal/mol
Surface area36680 Å2
MethodPISA
6
C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein

C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein

C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)121,52112
Polymers121,52112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area28300 Å2
ΔGint-212 kcal/mol
Surface area37480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.200, 69.200, 120.418
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11C-205-

HOH

21D-187-

HOH

31D-196-

HOH

41E-196-

HOH

51E-219-

HOH

61F-208-

HOH

71G-193-

HOH

81H-240-

HOH

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Components

#1: Protein
Microcompartments protein / Bacterial microcompartment


Mass: 10126.718 Da / Num. of mol.: 8
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_5815 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1 M ammonium tartrate, pH 6.5, 4% (v/v) formamide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.5
ReflectionResolution: 1.798→33.35 Å / Num. obs: 118444 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2.2 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I6P

3i6p


Resolution: 1.798→33.35 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.71 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2024 3.42 %Random selection
Rwork0.1704 ---
obs0.1757 118444 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.798→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5452 0 0 991 6443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035516
X-RAY DIFFRACTIONf_angle_d0.7267474
X-RAY DIFFRACTIONf_dihedral_angle_d9.2431988
X-RAY DIFFRACTIONf_chiral_restr0.029893
X-RAY DIFFRACTIONf_plane_restr0.003985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8007-1.83180.31731800.28535235X-RAY DIFFRACTION87
1.8318-1.86510.29052070.2655749X-RAY DIFFRACTION96
1.8651-1.9010.32241950.24745686X-RAY DIFFRACTION96
1.901-1.93980.30242030.24555744X-RAY DIFFRACTION96
1.9398-1.98190.26892000.21595731X-RAY DIFFRACTION96
1.9819-2.0280.23381960.21035785X-RAY DIFFRACTION96
2.028-2.07870.20351900.20855690X-RAY DIFFRACTION96
2.0787-2.13490.19542080.19675725X-RAY DIFFRACTION96
2.1349-2.19770.20591860.19075738X-RAY DIFFRACTION96
2.1977-2.26860.24531940.19145775X-RAY DIFFRACTION96
2.2686-2.34970.2231990.17985797X-RAY DIFFRACTION96
2.3497-2.44370.19512000.17325746X-RAY DIFFRACTION96
2.4437-2.55490.20022160.16465741X-RAY DIFFRACTION96
2.5549-2.68950.19442080.16495737X-RAY DIFFRACTION96
2.6895-2.85790.20162060.15865738X-RAY DIFFRACTION96
2.8579-3.07840.18442020.15495721X-RAY DIFFRACTION96
3.0784-3.38780.18751990.14875766X-RAY DIFFRACTION96
3.3878-3.87710.17412310.14915697X-RAY DIFFRACTION96
3.8771-4.88140.14612040.11945780X-RAY DIFFRACTION96
4.8814-30.10870.26421980.17595784X-RAY DIFFRACTION97

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