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- PDB-6mpr: Crystal structure of a malonate decarboxylase, alpha subunit from... -

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Basic information

Entry
Database: PDB / ID: 6mpr
TitleCrystal structure of a malonate decarboxylase, alpha subunit from Acinetobacter baumannii
ComponentsMalonate decarboxylase subunit alpha
KeywordsLYASE / structural genomics / NIAID / rod-shaped / coccobacillus / Gram-negative bacterium / malonic acid / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyAcetyl-S-ACP:malonate ACP transferase / Malonate decarboxylase, alpha subunit, transporter / NagB/RpiA transferase-like / transferase activity / Malonate decarboxylase subunit alpha
Function and homology information
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a malonate decarboxylase, alpha subunit from Acinetobacter baumannii
Authors: Edwards, T.E. / Mayclin, S.J. / Horanyi, P.S. / Lorimer, D.D.
History
DepositionOct 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Malonate decarboxylase subunit alpha
B: Malonate decarboxylase subunit alpha


Theoretical massNumber of molelcules
Total (without water)125,7862
Polymers125,7862
Non-polymers00
Water21,9061216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-29 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.370, 120.320, 75.040
Angle α, β, γ (deg.)90.000, 112.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Malonate decarboxylase subunit alpha


Mass: 62892.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Strain: ATCC 17978 / NCDC KC 755 / Gene: ABO11849 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3M5S3, EC: 4.1.1.89
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1216 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.09 mg/mL AcbaB.17485.a.PW38403 against JCSG+ screen condition A12 (0.2 M potassium nitrate, 20% PEG3350), crystal tracking ID 299425a12, unique puck ID aas7-10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→45.399 Å / Num. obs: 119022 / % possible obs: 96.9 % / Redundancy: 4.577 % / Biso Wilson estimate: 26.808 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.069 / Χ2: 1.021 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.744.7190.5932.4987330.840.66896.6
1.74-1.794.7780.4263.2485610.9140.47997.1
1.79-1.844.7730.3264.2183720.9420.36797.3
1.84-1.94.5380.3074.9879970.9510.34995.6
1.9-1.963.9880.2196.7772180.9820.25589.6
1.96-2.034.7580.1678.2176470.9840.18897.7
2.03-2.114.2320.1569.3772030.9830.17995.8
2.11-2.194.7470.11512.0471780.9910.12998.2
2.19-2.294.3630.09513.8865390.9920.10994
2.29-2.44.7540.07916.4765600.9950.08998.2
2.4-2.534.7360.0718.3962480.9960.07998.7
2.53-2.694.5280.06520.1358380.9960.07397.8
2.69-2.874.6790.05224.0656130.9970.05898.8
2.87-3.14.6820.04427.5352030.9980.04999
3.1-3.44.6450.03731.8648110.9980.04299.2
3.4-3.84.1930.03733.2543040.9980.04298
3.8-4.394.4090.03236.0337960.9980.03698
4.39-5.384.6590.02838.5932610.9990.03299.5
5.38-7.64.6120.0337.1525460.9990.03499.4
7.6-45.3994.4780.03139.7613940.9980.03598.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VIT

5vit


Resolution: 1.7→45.399 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.3
RfactorNum. reflection% reflection
Rfree0.1967 6792 6.07 %
Rwork0.1588 --
obs0.1611 111975 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.11 Å2 / Biso mean: 21.8082 Å2 / Biso min: 6.75 Å2
Refinement stepCycle: final / Resolution: 1.7→45.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8388 0 0 1223 9611
Biso mean---33.09 -
Num. residues----1088
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.31831890.2693057324680
1.7193-1.73950.28311940.25473056325080
1.7395-1.76070.27242360.23283227346385
1.7607-1.7830.2822280.21783323355187
1.783-1.80650.2792130.20743367358088
1.8065-1.83120.25212330.19773418365189
1.8312-1.85740.23182140.19923366358089
1.8574-1.88510.30612080.25923216342484
1.8851-1.91460.27011880.26652849303775
1.9146-1.9460.30481860.26532854304075
1.946-1.97950.252220.20083378360088
1.9795-2.01550.20112150.17343578379393
2.0155-2.05430.24172020.1773505370791
2.0543-2.09620.22182270.2033387361488
2.0962-2.14180.20792090.15953647385694
2.1418-2.19160.18182510.15663618386996
2.1916-2.24640.19742260.16263478370491
2.2464-2.30710.222060.16093481368791
2.3071-2.3750.20162450.14643736398197
2.375-2.45170.19552640.14563718398297
2.4517-2.53930.19732420.14963748399098
2.5393-2.6410.17332430.15083766400998
2.641-2.76110.21342320.15853689392196
2.7611-2.90670.19652570.14993783404099
2.9067-3.08880.17592420.15213820406299
3.0888-3.32720.1662420.14513813405599
3.3272-3.66190.17922520.14253751400398
3.6619-4.19140.15692440.12633785402998
4.1914-5.27950.15072330.105738754108100
5.2795-45.41490.14632490.13183894414399
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)
10.2128-0.65310.30142.4151-1.91552.8641-0.198-0.249-0.06370.38910.22770.2491-0.24-0.2524-0.03870.17260.05190.03840.2418-0.01890.1226-2.9794-4.98149.1881
24.45020.8692-0.53221.9509-0.75622.2611-0.0916-0.122-0.10480.09630.0340.09120.2036-0.18040.06970.1135-0.01670.00940.0737-0.01230.07542.6851-16.968138.5681
32.58910.142-0.89774.18770.64343.9444-0.0282-0.0136-0.22020.2176-0.01950.1250.4871-0.15170.03530.1276-0.0237-0.01160.08450.00630.12481.5489-25.211930.8272
40.9187-0.0961-0.28120.42450.03930.7943-0.0632-0.0389-0.06190.01640.0421-0.09540.03830.0530.01310.0879-0.0075-0.01990.0541-0.00830.122521.8463-11.384729.124
50.70510.1839-0.00431.22140.06840.5574-0.03960.126-0.0546-0.16150.0688-0.03210.1047-0.0703-0.03280.1125-0.0314-0.00430.1213-0.02140.103215.2858-14.863110.1075
60.7851-0.3402-0.91491.13740.11391.14-0.10440.2918-0.0615-0.26440.0443-0.09140.1775-0.27720.04110.195-0.07910.02180.2313-0.04680.139619.9355-23.0884-0.3733
72.1132-0.09280.06342.6921.45825.8145-0.1012-0.0528-0.24770.12260.0598-0.28280.450.40970.03260.14650.046-0.01950.08470.01610.258537.7074-24.422426.4411
81.23220.3070.24551.06960.28280.7135-0.10980.0780.1652-0.11560.0767-0.0986-0.24540.07330.01260.1702-0.0323-0.02930.07670.0140.146224.735115.630425.9515
90.5096-0.03310.08420.05430.10740.221-0.05640.10230.25-0.098-0.03460.0264-0.1992-0.0740.08720.2530.0476-0.05370.14150.01510.19144.309116.212623.1082
101.0193-0.12270.33980.72370.02061.4196-0.05150.00030.0776-0.03-0.00580.1542-0.226-0.28070.0490.13080.0536-0.03020.15760.00110.1441-7.33488.160122.4249
110.7416-0.0660.20580.7493-0.21371.1179-0.08390.20990.021-0.18380.03130.0027-0.1388-0.05260.0160.1401-0.0157-0.03010.1612-0.00490.10714.36571.71276.4426
122.10070.36711.43730.7845-0.0191.7468-0.07870.25570.0389-0.12530.01680.0852-0.1679-0.13230.03560.18080.0088-0.04360.2596-0.01050.1075-3.94452.9244-4.7294
133.4043-0.76371.20583.8350.73484.1425-0.20520.1280.17110.00210.01870.1489-0.5501-0.23250.18080.30280.1523-0.03420.21110.02040.2394-13.98720.749719.1227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 47 )A10 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 91 )A48 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 123 )A92 - 123
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 339 )A124 - 339
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 450 )A340 - 450
6X-RAY DIFFRACTION6chain 'A' and (resid 451 through 525 )A451 - 525
7X-RAY DIFFRACTION7chain 'A' and (resid 526 through 557 )A526 - 557
8X-RAY DIFFRACTION8chain 'B' and (resid 11 through 200 )B11 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 248 )B201 - 248
10X-RAY DIFFRACTION10chain 'B' and (resid 249 through 339 )B249 - 339
11X-RAY DIFFRACTION11chain 'B' and (resid 340 through 450 )B340 - 450
12X-RAY DIFFRACTION12chain 'B' and (resid 451 through 525 )B451 - 525
13X-RAY DIFFRACTION13chain 'B' and (resid 526 through 553 )B526 - 553

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