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- PDB-4qiv: Crystal structure of hexameric microcomparment shell protein from... -

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Basic information

Entry
Database: PDB / ID: 4qiv
TitleCrystal structure of hexameric microcomparment shell protein from Aeromonas hydrophila
ComponentsBacterial microcompartments family protein
KeywordsSTRUCTURAL PROTEIN / BMC domain
Function / homology
Function and homology information


BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartments family protein
Similarity search - Component
Biological speciesAeromonas hydrophila subsp. hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPang, A.H. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: To be Published
Title: Crystal structure of a hexameric microcomparment protein from Aeromonas hydrophila
Authors: Pang, A.H. / Sawaya, M.R. / Yeates, T.O.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial microcompartments family protein
B: Bacterial microcompartments family protein
C: Bacterial microcompartments family protein


Theoretical massNumber of molelcules
Total (without water)35,3293
Polymers35,3293
Non-polymers00
Water82946
1
A: Bacterial microcompartments family protein
B: Bacterial microcompartments family protein
C: Bacterial microcompartments family protein

A: Bacterial microcompartments family protein
B: Bacterial microcompartments family protein
C: Bacterial microcompartments family protein


Theoretical massNumber of molelcules
Total (without water)70,6596
Polymers70,6596
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area9500 Å2
ΔGint-89 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.460, 115.210, 122.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11C-111-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 3 - 88 / Label seq-ID: 23 - 108

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Bacterial microcompartments family protein


Mass: 11776.442 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila (bacteria)
Strain: ATCC 7966 / NCIB 9240 / Gene: AHA_1335 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0KHX4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.66 Å3/Da / Density % sol: 25.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 1.5M Ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2013
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.298→61.2 Å / Num. all: 6835 / Num. obs: 6835 / % possible obs: 64 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.96
Reflection shellResolution: 2.298→2.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 7.85 / % possible all: 14.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.603
Highest resolutionLowest resolution
Rotation61.18 Å2.54 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→61.17 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.838 / SU B: 8.513 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27541 327 4.8 %RANDOM
Rwork0.22131 ---
obs0.22381 6508 63.97 %-
all-6835 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 0 46 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191819
X-RAY DIFFRACTIONr_bond_other_d0.0030.021864
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9782465
X-RAY DIFFRACTIONr_angle_other_deg0.98834276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.86226.42956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00515314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.091157
X-RAY DIFFRACTIONr_chiral_restr0.0730.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0791.8041034
X-RAY DIFFRACTIONr_mcbond_other3.0571.7961033
X-RAY DIFFRACTIONr_mcangle_it4.8482.6751289
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1782.543785
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A48470.09
12B48470.09
21A49470.08
22C49470.08
31B48020.1
32C48020.1
LS refinement shellResolution: 2.298→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.136 115 -
Rfree-0 -
obs--14.78 %

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