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- PDB-6nds: Structure of an HMG-CoA lyase from Acenitobacter baumannii in com... -

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Basic information

Entry
Database: PDB / ID: 6nds
TitleStructure of an HMG-CoA lyase from Acenitobacter baumannii in complex with coenzyme A and 3-methylmalate
Components3-hydroxy-3-methylglutaryl-CoA lyase
KeywordsLYASE / SSGCID / Acinetobacter baumannii / 3-hydroxy-3-methylglutaryl-CoA / CoA / beta-methylmalate / HMG / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity
Similarity search - Function
HMG-CoA lyase / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / COENZYME A / 3-hydroxy-3-methylglutaryl-CoA lyase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of an HMG-CoA lyase from Acenitobacter baumannii in complex with coenzyme A and 3-methylmalate
Authors: Mayclin, S.J. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-hydroxy-3-methylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0838
Polymers34,8191
Non-polymers1,2647
Water4,810267
1
A: 3-hydroxy-3-methylglutaryl-CoA lyase
hetero molecules

A: 3-hydroxy-3-methylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,16616
Polymers69,6372
Non-polymers2,52914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7540 Å2
ΔGint-85 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.460, 91.460, 78.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-hydroxy-3-methylglutaryl-CoA lyase / Hydroxymethylglutaryl-CoA lyase / Hydroxymethylglutaryl-CoA lyase YngG


Mass: 34818.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: yngG_1, ABUW_2506, CBI29_01513, DV997_16665 / Plasmid: AcbaC.18886.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D5YK08, hydroxymethylglutaryl-CoA lyase

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Non-polymers , 6 types, 274 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Top96 D11 (298571d11): 2 0.1 M Sodium Acetate: HCl, pH 4.6, 8% (w/v) PEG4000, 4mM NAD (bsi1606), 4mM HMG-CoA (bsi108595); AcbaC.18179.a.B1.PW38191 conc 23.33mg/mL; 20eg; puck/pin ID tud0-16

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45.73 Å / Num. obs: 40790 / % possible obs: 100 % / Redundancy: 8.605 % / Biso Wilson estimate: 31.195 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 1.003 / Net I/σ(I): 20.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.696.240.5622.9129600.8520.61399.7
1.69-1.748.0180.4914.1528860.9190.525100
1.74-1.799.1840.3725.8528250.9680.395100
1.79-1.849.1450.2667.8827380.9820.281100
1.84-1.918.9710.19610.2326680.9880.208100
1.91-1.978.6160.15512.6425650.9920.165100
1.97-2.058.9430.11516.1924870.9950.122100
2.05-2.139.1690.10119.0324050.9960.107100
2.13-2.229.0940.08122.6723000.9970.086100
2.22-2.338.5220.07125.2921990.9970.07599.9
2.33-2.468.7390.06427.4721150.9980.068100
2.46-2.619.20.05831.0419910.9980.06299.9
2.61-2.799.0470.05433.6318680.9980.057100
2.79-3.018.5440.0535.5217690.9980.05499.9
3.01-3.38.6550.04738.8616340.9980.05100
3.3-3.698.9780.04442.2214800.9990.04799.9
3.69-4.268.4840.04243.0913150.9990.04599.9
4.26-5.228.3040.04343.311460.9980.046100
5.22-7.388.3230.04541.998970.9990.048100
7.38-507.4630.04142.075420.9980.04499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
Cootmodel building
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→45.73 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1677 2379 6.03 %
Rwork0.1532 37070 -
obs0.1541 39449 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.78 Å2 / Biso mean: 29.1193 Å2 / Biso min: 13.4 Å2
Refinement stepCycle: final / Resolution: 1.65→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 75 268 2620
Biso mean--44.23 38.78 -
Num. residues----305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6499-1.68360.30941210.2398192387
1.6836-1.72020.22161370.2106200991
1.7202-1.76020.21861410.1782202292
1.7602-1.80430.17761170.1618210694
1.8043-1.85310.18751550.1542208195
1.8531-1.90760.1471200.1503215196
1.9076-1.96920.18771460.1601215697
1.9692-2.03950.19951390.149217398
2.0395-2.12120.17161410.1526221598
2.1212-2.21770.1411360.1426222499
2.2177-2.33460.18351380.1397221798
2.3346-2.48090.18071500.1497222399
2.4809-2.67240.16421430.15212252100
2.6724-2.94130.18451350.15432279100
2.9413-3.36680.16471490.15442284100
3.3668-4.24140.15421490.13952306100
4.2414-500.14691620.15922449100
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)
13.3207-1.64351.73253.1558-0.99992.62990.01180.0921-0.0416-0.09810.03570.0945-0.01610.048-0.04670.1201-0.02440.02630.1110.00130.1177-11.425931.69064.3439
21.04630.97480.15683.370.11651.7179-0.09430.24120.0935-0.36050.07040.04690.02110.0509-0.00850.1988-0.01430.01250.21670.00140.1478-10.552127.6572-6.3483
30.94190.35890.1941.424-0.36151.8767-0.05810.265-0.142-0.35850.0805-0.11770.29120.0037-0.00850.23930.01520.03220.203-0.05260.18-10.099312.8009-2.1001
41.9177-0.3522-0.39992.6005-0.05061.690.0147-0.05170.09190.1175-0.02240.1303-0.0654-0.12390.00160.11890.0016-0.00380.1452-0.00680.1432-11.360325.135817.2768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )A1 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 117 )A63 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 214 )A118 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 305 )A215 - 305

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