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- PDB-4qie: Crystal Structure of PduA with edge mutation K26D -

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Basic information

Entry
Database: PDB / ID: 4qie
TitleCrystal Structure of PduA with edge mutation K26D
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / BMC domain / Glycerol / sulfate ion
Function / homology
Function and homology information


propanediol degradation polyhedral organelle / propanediol catabolic process
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 shell protein PduA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3501 Å
AuthorsPang, A.H. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: To be Published
Title: Crystal Structure of PduA with edge mutation K26D
Authors: Pang, A.H. / Sawaya, M.R. / Bobik, T.A. / Yeates, T.O.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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_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: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
H: Propanediol utilization protein PduA
I: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,66614
Polymers95,1949
Non-polymers4725
Water1,11762
1
A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7479
Polymers63,4636
Non-polymers2843
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-71 kcal/mol
Surface area19730 Å2
MethodPISA
2
G: Propanediol utilization protein PduA
H: Propanediol utilization protein PduA
I: Propanediol utilization protein PduA
hetero molecules

G: Propanediol utilization protein PduA
H: Propanediol utilization protein PduA
I: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,83910
Polymers63,4636
Non-polymers3764
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area9450 Å2
ΔGint-72 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.110, 108.110, 334.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10577.102 Da / Num. of mol.: 9 / Mutation: K26D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: pduA, STM2038 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1C7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tri-sodium citrate, 2.4M ammonium sulfate, pH 9, 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: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2013
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→19.85 Å / Num. all: 46445 / Num. obs: 46445 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 6.87 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.09
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.64 / Num. unique all: 3005 / % possible all: 84.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phaser-mr)model building
PHENIX(phenix.refine: dev_1555)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(phaser-mr)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NGK

3ngk


Resolution: 2.3501→19.847 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 4643 10 %Random
Rwork0.2014 ---
obs0.2052 46439 94.63 %-
all-46439 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.6984 Å2
Refinement stepCycle: LAST / Resolution: 2.3501→19.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 27 62 5582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095577
X-RAY DIFFRACTIONf_angle_d1.2827572
X-RAY DIFFRACTIONf_dihedral_angle_d11.6341988
X-RAY DIFFRACTIONf_chiral_restr0.052961
X-RAY DIFFRACTIONf_plane_restr0.007975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.37670.29051320.26411183X-RAY DIFFRACTION83
2.3767-2.40460.28341400.26681259X-RAY DIFFRACTION86
2.4046-2.43390.35751340.26251208X-RAY DIFFRACTION86
2.4339-2.46470.32991410.2581268X-RAY DIFFRACTION86
2.4647-2.4970.28561350.24911218X-RAY DIFFRACTION86
2.497-2.53120.28191410.24411264X-RAY DIFFRACTION86
2.5312-2.56730.31771360.24711227X-RAY DIFFRACTION86
2.5673-2.60550.31191380.25741239X-RAY DIFFRACTION86
2.6055-2.64610.29931380.24731247X-RAY DIFFRACTION86
2.6461-2.68940.29581370.25311235X-RAY DIFFRACTION85
2.6894-2.73570.29111520.23821361X-RAY DIFFRACTION95
2.7357-2.78530.26181630.23631468X-RAY DIFFRACTION100
2.7853-2.83870.26461630.23651466X-RAY DIFFRACTION100
2.8387-2.89650.2921570.23821421X-RAY DIFFRACTION100
2.8965-2.95920.27121600.241438X-RAY DIFFRACTION99
2.9592-3.02780.29751640.24551472X-RAY DIFFRACTION100
3.0278-3.10330.26981610.23811448X-RAY DIFFRACTION100
3.1033-3.18690.29281640.2361478X-RAY DIFFRACTION100
3.1869-3.28020.24771620.23591462X-RAY DIFFRACTION100
3.2802-3.38560.28671620.21381457X-RAY DIFFRACTION100
3.3856-3.5060.22531620.2081456X-RAY DIFFRACTION100
3.506-3.64550.21451630.19191467X-RAY DIFFRACTION99
3.6455-3.81030.20831620.17981463X-RAY DIFFRACTION99
3.8103-4.00970.21681650.18191482X-RAY DIFFRACTION99
4.0097-4.25860.17581640.16821473X-RAY DIFFRACTION99
4.2586-4.58360.23151660.16251495X-RAY DIFFRACTION99
4.5836-5.03810.20211660.1561498X-RAY DIFFRACTION99
5.0381-5.75150.22441680.1761512X-RAY DIFFRACTION98
5.7515-7.18860.23261710.18851545X-RAY DIFFRACTION98
7.1886-19.84820.15991760.15641586X-RAY DIFFRACTION95

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