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- PDB-6ci8: Structure of the microcompartment-associated aminoacetone dehydro... -

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Basic information

Entry
Database: PDB / ID: 6ci8
TitleStructure of the microcompartment-associated aminoacetone dehydrogenase
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / dehydrogenase / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding
Similarity search - Function
: / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase MabA
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMallette, E. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: Biochemistry / Year: 2018
Title: Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis.
Authors: Mallette, E. / Kimber, M.S.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2524
Polymers54,1812
Non-polymers712
Water10,881604
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5038
Polymers108,3614
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area18260 Å2
ΔGint-182 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.240, 104.240, 80.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

21B-635-

HOH

31B-638-

HOH

41B-652-

HOH

51B-697-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 27090.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0269 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0QP46, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→45.137 Å / Num. obs: 56008 / % possible obs: 100 % / Redundancy: 6.208 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.06 / Χ2: 0.977 / Net I/σ(I): 19.86 / Num. measured all: 347712 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.746.2060.683.0440710.8650.741100
1.74-1.796.2070.5133.8940110.9070.558100
1.79-1.846.210.4034.9438960.9460.439100
1.84-1.96.2160.296.6638020.9690.316100
1.9-1.966.2370.2258.4536700.9810.246100
1.96-2.036.2510.16910.7735420.9880.185100
2.03-2.116.2260.1313.6834100.9920.142100
2.11-2.196.2530.10516.4133220.9950.115100
2.19-2.296.2430.0918.5631530.9960.09999.9
2.29-2.46.2380.07521.5930580.9960.083100
2.4-2.536.270.06424.5429040.9970.07100
2.53-2.696.2530.05528.0327320.9970.06199.9
2.69-2.876.2650.04631.7925770.9980.051100
2.87-3.16.2310.04335.5824070.9980.04799.9
3.1-3.46.2120.03640.8822130.9980.03999.9
3.4-3.86.1520.03244.720120.9980.03699.9
3.8-4.396.1380.03147.4818010.9980.03499.9
4.39-5.386.0970.03148.0715240.9990.03499.9
5.38-7.65.9420.0347.0712020.9980.03499.9
7.6-45.1375.5380.03148.217010.9990.03599.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIH

3rih


Resolution: 1.7→45.137 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.51
RfactorNum. reflection% reflection
Rfree0.1698 2801 5 %
Rwork0.1442 --
obs0.1454 56008 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.49 Å2 / Biso mean: 23.5985 Å2 / Biso min: 6.63 Å2
Refinement stepCycle: final / Resolution: 1.7→45.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 2 604 4388
Biso mean--24.57 32.64 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173914
X-RAY DIFFRACTIONf_angle_d1.3335341
X-RAY DIFFRACTIONf_chiral_restr0.1639
X-RAY DIFFRACTIONf_plane_restr0.008709
X-RAY DIFFRACTIONf_dihedral_angle_d8.4923121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.72930.25541370.213226042741
1.7293-1.76080.24711400.198626492789
1.7608-1.79460.20471390.180426462785
1.7946-1.83130.20591390.172526492788
1.8313-1.87110.17651370.15726072744
1.8711-1.91460.19151400.150826512791
1.9146-1.96250.18161390.150726442783
1.9625-2.01560.1771390.143726392778
2.0156-2.07490.18521380.145326222760
2.0749-2.14180.16831390.13826412780
2.1418-2.21840.17371400.132526572797
2.2184-2.30720.16271400.135826592799
2.3072-2.41220.16811390.13226382777
2.4122-2.53940.1611410.140726842825
2.5394-2.69840.16621390.141726512790
2.6984-2.90680.18281410.143726722813
2.9068-3.19920.16491410.14426792820
3.1992-3.6620.14061420.135826942836
3.662-4.6130.13491420.123627002842
4.613-45.15310.17791490.149728232972
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4225-0.0345-0.65371.5683-0.57621.6086-0.0515-0.2924-0.14680.05730.10120.2910.0194-0.3599-0.0010.0558-0.01460.01860.24840.02330.192210.779876.007743.4233
22.84591.20260.49812.72381.32574.2692-0.09650.1186-0.3731-0.06290.10.3810.2691-0.45430.00360.0882-0.0492-0.00780.2963-0.00570.31263.250473.809333.4246
33.28140.0983-2.56681.4087-0.28433.28090.0783-0.0395-0.0565-0.04640.04680.39040.0183-0.3978-0.05150.0482-0.0396-0.00970.2830.01590.26465.677477.347933.7491
40.9081-0.3770.21160.9958-0.18830.52410.03010.1014-0.0696-0.0959-0.01580.16090.1001-0.12040.0020.0785-0.0318-0.00980.1453-0.01450.112421.193773.211329.7877
52.36390.4682-0.67712.9647-0.66721.9337-0.09960.1314-0.3989-0.38940.10860.47280.3735-0.41280.13220.1251-0.0814-0.05440.1977-0.00540.240816.384864.294438.4106
61.95420.71970.24173.58460.07122.37780.03230.1442-0.8779-0.3566-0.0440.39870.7169-0.52580.00710.308-0.17820.00310.2672-0.00230.477315.424950.380643.3957
72.46540.97370.29921.6647-0.06430.8475-0.0184-0.22520.03790.0828-0.00690.11970.0425-0.23740.00840.084-0.00490.01460.163-0.01010.10421.138675.191446.9303
82.3418-0.34760.31068.4550.04291.9183-0.0701-0.0937-0.58230.00440.11610.08630.4591-0.2066-0.06180.1915-0.07670.03110.1420.00990.192327.810553.68244.9468
92.324-1.02640.51231.5160.47562.02730.21480.66310.1692-0.4013-0.2651-0.22420.11530.3520.02610.30640.1020.0640.3401-0.0050.123551.133761.488112.5117
104.9511-1.1372-1.49910.88660.91321.48410.09110.37230.089-0.4009-0.1556-0.1790.11560.2059-0.01810.37140.13820.0810.50030.00790.116847.350462.49017.1577
111.1526-0.6281-0.01861.4074-0.09280.43290.16020.4895-0.0105-0.3396-0.17480.04220.18150.04330.04780.26320.0431-0.02120.2582-0.05830.075335.733463.704714.5832
121.2835-0.40110.33881.52840.65491.41740.08530.2416-0.0233-0.1388-0.0715-0.07310.15090.03630.02120.11810.00850.00790.1083-0.01020.063740.285465.200825.591
131.78060.50.03662.3571-0.06141.56260.03030.10920.2421-0.1181-0.084-0.0898-0.07770.0950.02970.08550.02740.00280.08490.02950.119450.671168.67232.5336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A1 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 50 )A30 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 67 )A51 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 178 )A68 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 199 )A179 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 217 )A200 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 238 )A218 - 238
8X-RAY DIFFRACTION8chain 'A' and (resid 239 through 258 )A239 - 258
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 50 )B1 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 67 )B51 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 133 )B68 - 133
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 199 )B134 - 199
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 258 )B200 - 258

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