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- PDB-3nwg: The crystal structure of a microcomparments protein from Desulfit... -

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Basic information

Entry
Database: PDB / ID: 3nwg
TitleThe crystal structure of a microcomparments protein from Desulfitobacterium hafniense DCB
ComponentsMicrocompartments protein
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / BMC domain
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
Microcompartments protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsFan, Y. / Volkart, L. / Gu, M. / Axen, S. / Greenleaf, W.B. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a PduT homolog from a novel bacterial microcompartment
Authors: Greenleaf, W.B. / Fan, Y. / Axen, S. / Volkart, L. / Gu, M. / Joachimiak, A. / Kerfeld, C.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2344
Polymers18,9571
Non-polymers2763
Water64936
1
A: Microcompartments protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)115,40124
Polymers113,7446
Non-polymers1,65818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area16220 Å2
ΔGint-85 kcal/mol
Surface area39840 Å2
MethodPISA
2
A: Microcompartments protein
hetero molecules

A: Microcompartments protein
hetero molecules

A: Microcompartments protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,70112
Polymers56,8723
Non-polymers8299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6110 Å2
ΔGint-33 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.862, 104.862, 81.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsSize exclusion chromatography confirms the presence of trimers. Two copies of trimer can potentially stack together and form a hexamer, as found in crystal lattice.

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Components

#1: Protein Microcompartments protein


Mass: 18957.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB / Gene: Dhaf_0360 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: B8G1Q4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (w/v) PEG400, 0.2M magnesium chloride, 0.1M HEPES at pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 7665 / Num. obs: 7665 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 54.77 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 53.1
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 4.63 / Num. unique all: 193 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
SHELXDphasing
MLPHAREphasing
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 25.201 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28301 369 4.9 %RANDOM
Rwork0.2227 ---
all0.22586 7239 --
obs0.22586 7239 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.863 Å2
Baniso -1Baniso -2Baniso -3
1--3.48 Å2-1.74 Å20 Å2
2---3.48 Å20 Å2
3---5.22 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1287 0 18 36 1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221316
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9951784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.12125.55636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11715225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.906154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021913
X-RAY DIFFRACTIONr_mcbond_it0.8461.5892
X-RAY DIFFRACTIONr_mcangle_it1.57121438
X-RAY DIFFRACTIONr_scbond_it1.6223424
X-RAY DIFFRACTIONr_scangle_it2.9324.5346
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 35 -
Rwork0.253 497 -
obs--96.55 %
Refinement TLS params.Method: refined / Origin x: 0.6729 Å / Origin y: 40.8598 Å / Origin z: 37.235 Å
111213212223313233
T0.0141 Å20.016 Å2-0.0107 Å2-0.0279 Å20.0049 Å2--0.0847 Å2
L5.8447 °2-0.0761 °20.229 °2-0.7022 °20.1379 °2--0.065 °2
S0.0283 Å °-0.0682 Å °-0.0186 Å °-0.0084 Å °-0.0079 Å °0.0321 Å °0.0078 Å °-0.0079 Å °-0.0204 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 79
2X-RAY DIFFRACTION1A95 - 171

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