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- PDB-4qig: Crystal Structure of PduA with edge mutation K26A and pore mutati... -

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Basic information

Entry
Database: PDB / ID: 4qig
TitleCrystal Structure of PduA with edge mutation K26A and pore mutation S40C
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / BMC domain / sulfate ion
Function / homology
Function and homology information


propanediol degradation polyhedral organelle / 1,2-propanediol catabolic process
Similarity search - Function
BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily ...BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / 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
Bacterial microcompartment shell protein PduA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.297 Å
AuthorsPang, A.H. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Selective molecular transport through the protein shell of a bacterial microcompartment organelle.
Authors: Chowdhury, C. / Chun, S. / Pang, A. / Sawaya, M.R. / Sinha, S. / Yeates, T.O. / Bobik, T.A.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4Sep 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_conn / struct_ncs_dom_lim / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0369
Polymers73,8447
Non-polymers1922
Water00
1
A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
hetero molecules

A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
hetero molecules

A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5839
Polymers63,2956
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area9890 Å2
ΔGint-103 kcal/mol
Surface area20060 Å2
MethodPISA
2
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA

C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA

C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA


Theoretical massNumber of molelcules
Total (without water)63,2956
Polymers63,2956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9730 Å2
ΔGint-94 kcal/mol
Surface area20010 Å2
MethodPISA
3
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
hetero molecules

E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
G: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4878
Polymers63,2956
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
Buried area9620 Å2
ΔGint-94 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.440, 235.440, 235.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROAA3 - 8911 - 97
21GLNGLNPROPROBB3 - 8911 - 97
12GLUGLULYSLYSAA4 - 9012 - 98
22GLUGLULYSLYSCC4 - 9012 - 98
13GLUGLULYSLYSAA4 - 9012 - 98
23GLUGLULYSLYSDD4 - 9012 - 98
14ALAALALEULEUAA5 - 8813 - 96
24ALAALALEULEUEE5 - 8813 - 96
15ALAALALEULEUAA5 - 8813 - 96
25ALAALALEULEUFF5 - 8813 - 96
16GLUGLUPROPROAA4 - 8912 - 97
26GLUGLUPROPROGG4 - 8912 - 97
17GLUGLUPROPROBB4 - 8912 - 97
27GLUGLUPROPROCC4 - 8912 - 97
18GLUGLUPROPROBB4 - 8912 - 97
28GLUGLUPROPRODD4 - 8912 - 97
19ALAALALEULEUBB5 - 8813 - 96
29ALAALALEULEUEE5 - 8813 - 96
110ALAALALEULEUBB5 - 8813 - 96
210ALAALALEULEUFF5 - 8813 - 96
111GLUGLUPROPROBB4 - 8912 - 97
211GLUGLUPROPROGG4 - 8912 - 97
112GLUGLUGLYGLYCC4 - 9112 - 99
212GLUGLUGLYGLYDD4 - 9112 - 99
113ALAALALEULEUCC5 - 8813 - 96
213ALAALALEULEUEE5 - 8813 - 96
114ALAALALEULEUCC5 - 8813 - 96
214ALAALALEULEUFF5 - 8813 - 96
115GLUGLUPROPROCC4 - 8912 - 97
215GLUGLUPROPROGG4 - 8912 - 97
116ALAALALEULEUDD5 - 8813 - 96
216ALAALALEULEUEE5 - 8813 - 96
117ALAALALEULEUDD5 - 8813 - 96
217ALAALALEULEUFF5 - 8813 - 96
118GLUGLUPROPRODD4 - 8912 - 97
218GLUGLUPROPROGG4 - 8912 - 97
119ALAALAPROPROEE5 - 8913 - 97
219ALAALAPROPROFF5 - 8913 - 97
120ALAALALEULEUEE5 - 8813 - 96
220ALAALALEULEUGG5 - 8813 - 96
121ALAALALEULEUFF5 - 8813 - 96
221ALAALALEULEUGG5 - 8813 - 96

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10549.157 Da / Num. of mol.: 7 / Fragment: Propanediol utilization protein pduA / Mutation: K26A, S40C
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 3.68 Å3/Da / Density % sol: 66.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5M Ammonium sulfate, 0.1M HEPES pH 7.5, 30% MPD, 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: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2014
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.297→83.24 Å / Num. all: 16403 / Num. obs: 16403 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.163 / Net I/σ(I): 32.47
Reflection shellResolution: 3.297→3.38 Å / Mean I/σ(I) obs: 4.24 / Num. unique all: 1218 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.3 Å83.24 Å
Translation3.3 Å83.24 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.5phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NGK

3ngk


Resolution: 3.297→83.24 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 17.948 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1637 10 %RANDOM
Rwork0.1889 ---
obs0.1932 16365 99.68 %-
all-16365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 245.4 Å2 / Biso mean: 94.737 Å2 / Biso min: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.297→83.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 0 10 0 4293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194336
X-RAY DIFFRACTIONr_bond_other_d0.0090.024484
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.9765887
X-RAY DIFFRACTIONr_angle_other_deg1.801310282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8865606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16924.922128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65315721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7791522
X-RAY DIFFRACTIONr_chiral_restr0.0980.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214880
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02790
X-RAY DIFFRACTIONr_mcbond_it8.3428.9582439
X-RAY DIFFRACTIONr_mcbond_other8.3388.9562438
X-RAY DIFFRACTIONr_mcangle_it12.46613.4393037
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A44090.16
12B44090.16
21A43860.14
22C43860.14
31A44340.14
32D44340.14
41A42230.15
42E42230.15
51A44130.11
52F44130.11
61A45340.13
62G45340.13
71B45790.14
72C45790.14
81B43710.16
82D43710.16
91B43780.16
92E43780.16
101B46590.11
102F46590.11
111B43850.16
112G43850.16
121C43590.15
122D43590.15
131C42800.15
132E42800.15
141C44810.12
142F44810.12
151C42630.16
152G42630.16
161D41670.16
162E41670.16
171D43360.12
172F43360.12
181D45730.12
182G45730.12
191E44520.12
192F44520.12
201E43020.15
202G43020.15
211F43750.13
212G43750.13
LS refinement shellResolution: 3.297→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 118 -
Rwork0.323 1062 -
all-1180 -
obs--99.92 %

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