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- PDB-9nzb: Crystal Structure of acyl-CoA lyase subunit beta from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 9nzb
TitleCrystal Structure of acyl-CoA lyase subunit beta from Pseudomonas aeruginosa PAO1
ComponentsAcyl-CoA lyase beta chain
KeywordsLYASE / Center for Structural Biology of Infectious Diseases / CSBID / acyl-CoA lyase / Structural Genomics
Function / homologyCitrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / oxaloacetate metabolic process / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / lyase activity / magnesium ion binding / Probable acyl-CoA lyase beta chain
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Shukla, S. / Shuvalova, L. / Brunzelle, J.S. / Warwzak, Z. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of acyl-CoA lyase subunit beta from Pseudomonas aeruginosa PAO1
Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Brunzelle, J.S. / Warwzak, Z. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA lyase beta chain
B: Acyl-CoA lyase beta chain
C: Acyl-CoA lyase beta chain
D: Acyl-CoA lyase beta chain
E: Acyl-CoA lyase beta chain
F: Acyl-CoA lyase beta chain


Theoretical massNumber of molelcules
Total (without water)175,9846
Polymers175,9846
Non-polymers00
Water23,4741303
1
A: Acyl-CoA lyase beta chain
B: Acyl-CoA lyase beta chain
C: Acyl-CoA lyase beta chain


Theoretical massNumber of molelcules
Total (without water)87,9923
Polymers87,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-21 kcal/mol
Surface area32630 Å2
MethodPISA
2
D: Acyl-CoA lyase beta chain
E: Acyl-CoA lyase beta chain
F: Acyl-CoA lyase beta chain


Theoretical massNumber of molelcules
Total (without water)87,9923
Polymers87,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-22 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.828, 198.038, 65.351
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-CoA lyase beta chain


Mass: 29330.590 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0883 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I562
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 18.0 mg/ml, 0.15M Sodium chloride, 0.01M Tris-HCl (pH 8.0); Screen: Classics II (G1), 0.2M Sodium chloride, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350; Cryo: Reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 134881 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.054 / Rrim(I) all: 0.095 / Rsym value: 0.077 / Χ2: 1.001 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2 / Num. unique obs: 5212 / CC1/2: 0.445 / Rpim(I) all: 0.517 / Rrim(I) all: 0.876 / Rsym value: 0.703 / Χ2: 0.995 / % possible all: 73.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.044 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20888 6719 5 %RANDOM
Rwork0.17228 ---
obs0.17416 126517 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å21.07 Å2
2--1.2 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.85→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11704 0 0 1303 13007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212202
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612113
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.83716622
X-RAY DIFFRACTIONr_angle_other_deg0.5641.75227701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.26551613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.7095156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.965101979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21911
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215159
X-RAY DIFFRACTIONr_gen_planes_other0.010.022813
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3080.8586392
X-RAY DIFFRACTIONr_mcbond_other1.3070.8586391
X-RAY DIFFRACTIONr_mcangle_it2.1571.5158025
X-RAY DIFFRACTIONr_mcangle_other2.1571.5168026
X-RAY DIFFRACTIONr_scbond_it2.0821.1735810
X-RAY DIFFRACTIONr_scbond_other2.0821.1735811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3742.0188598
X-RAY DIFFRACTIONr_long_range_B_refined8.39312.7314019
X-RAY DIFFRACTIONr_long_range_B_other8.3429.8113671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 345 -
Rwork0.242 8163 -
obs--82.67 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4341-0.6635-0.27582.48020.28251.4042-0.079-0.06720.0634-0.00930.0071-0.1380.03830.1240.07190.23370.0013-0.07230.13550.0020.26931.002-2.67331.732
20.9783-0.32250.0850.8755-0.07160.8085-0.0361-0.0093-0.0586-0.0330.04970.04650.0339-0.0453-0.01360.2605-0.0196-0.07510.13730.00560.28515.917-0.07227.5
31.1339-0.7141-0.1473.50320.34890.89190.0432-0.06220.17760.17310.0776-0.0837-0.0988-0.0251-0.12080.2929-0.008-0.03760.1303-0.00210.291221.83118.7532.036
47.2971-3.8173-3.75442.0882.603714.29050.4556-0.29110.0584-0.02820.1045-0.0410.7069-1.0681-0.560.5592-0.10030.05270.26310.03980.279614.03422.05445.611
51.9788-1.02911.02361.6801-0.56532.78090.08360.20290.1122-0.1895-0.0938-0.0656-0.06830.13830.01020.3091-0.0115-0.06110.17760.01240.2493-5.6790.657-9.679
60.68450.03410.21530.87860.24151.4374-0.02090.05480.0289-0.0076-0.01070.0175-0.03640.00070.03160.27740.0014-0.06360.1560.01150.2501-6.4031.3310.932
72.72110.4959-1.769510.3559-1.819312.59740.1212-0.04360.0075-0.1054-0.577-2.0658-0.2806-0.01090.45580.0141-0.00740.020.35620.0570.442523.313-3.488-3.292
85.607-3.73245.64928.6062-6.86699.1990.22610.1329-0.3420.2716-0.3445-0.91490.41710.68370.11840.2250.0292-0.12460.27360.01240.359615.939-6.0161.233
91.088-0.2150.12921.565-0.93333.317-0.0846-0.02360.21090.44330.1036-0.0188-0.6737-0.2452-0.0190.43990.1058-0.06330.12430.00640.3059-16.04929.71635.686
101.5195-0.06360.04671.1006-0.27361.4688-0.0434-0.15630.08060.20880.10050.036-0.2072-0.1899-0.0570.30260.0575-0.06360.1680.00670.2693-12.16518.30235.445
110.676-0.8344-0.36393.076-0.18584.87840.09360.15380.1027-0.27510.0571-0.1608-0.4035-0.2715-0.15070.31830.0131-0.02290.15350.03910.3002-13.2129.82417.066
124.7085-0.655-3.148411.19824.53923.6625-0.00150.566-0.5073-0.2635-0.45190.5242-0.1825-0.52810.45340.26740.0196-0.04630.283-0.03260.3286-22.9821.12511.835
131.9472-0.145-1.09961.6691-0.37464.1688-0.00160.298-0.3339-0.2666-0.1329-0.05880.4961-0.38170.13450.3187-0.01970.00750.163-0.04880.3212-47.82236.8458.837
143.64110.6318-1.58713.46120.79172.2805-0.1560.5392-0.5056-0.444-0.17720.07510.2695-0.46080.33320.3209-0.0412-0.04530.2814-0.11010.3076-53.11739.5214.052
151.4474-0.07370.00660.8250.05871.12620.01810.1016-0.051-0.0681-0.0048-0.02460.0441-0.0862-0.01330.27080.0001-0.01340.13130.00290.2952-41.96349.3915.135
161.0238-0.14850.51891.6091-0.81563.7435-0.046-0.1146-0.07750.22420.13430.00380.1287-0.3394-0.08830.29970.00610.00720.15580.02310.3049-47.01837.14130.683
175.5461-1.43591.64910.73834.76114.6703-0.3957-0.43270.41540.4470.16290.55680.0372-0.62630.23280.28090.09030.04520.2714-0.00970.3074-56.15545.4936.306
182.0040.1523-1.48761.9344-0.37342.41330.0338-0.31390.00910.15130.04740.040.04710.1379-0.08120.3352-0.02140.0030.1684-0.01030.2397-44.85667.3157.601
191.1558-0.3143-0.7340.6784-0.05461.4334-0.0194-0.1549-0.02750.03490.0125-0.02320.06340.0980.00690.3109-0.0142-0.00940.1566-0.00320.2906-37.65263.54344.028
202.65011.46361.047313.8224-8.97657.4424-0.085-0.0852-0.94240.17730.1309-1.0446-0.2084-0.1158-0.04590.03790.01230.10670.5291-0.05390.6151-10.2969.44152.43
214.09430.5179-4.023811.3433-7.16527.8843-0.0736-0.96710.52920.05180.0168-0.93370.0410.87150.05680.1001-0.02660.00050.4242-0.13210.4337-18.05470.80648.457
222.49020.3040.15772.5578-0.20220.9069-0.0791-0.04430.05180.0336-0.0079-0.2639-0.04640.01220.0870.2510.009-0.00040.1358-0.00130.3513-0.8769.61717.34
231.48340.4784-0.69290.89770.05030.8263-0.0510.01720.106-0.01910.05410.08190.03490.0671-0.00310.26370.0171-0.00960.1270.0120.3457-17.83368.27120.288
241.99160.91810.50674.22180.15231.2906-0.02040.0322-0.2147-0.17350.1453-0.29720.11230.0657-0.12480.25630.0243-0.00890.1258-0.00550.3285-9.43748.94218.243
256.44820.87466.49253.05035.617414.80540.334-0.0714-0.1125-0.3263-0.2056-0.0967-0.5252-0.9625-0.12850.42470.1505-0.0210.6315-0.01710.2214-17.28147.3094.783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 72
2X-RAY DIFFRACTION2A73 - 196
3X-RAY DIFFRACTION3A197 - 240
4X-RAY DIFFRACTION4A241 - 275
5X-RAY DIFFRACTION5B1 - 40
6X-RAY DIFFRACTION6B41 - 227
7X-RAY DIFFRACTION7B228 - 240
8X-RAY DIFFRACTION8B257 - 273
9X-RAY DIFFRACTION9C1 - 42
10X-RAY DIFFRACTION10C43 - 190
11X-RAY DIFFRACTION11C191 - 242
12X-RAY DIFFRACTION12C256 - 274
13X-RAY DIFFRACTION13D1 - 50
14X-RAY DIFFRACTION14D51 - 71
15X-RAY DIFFRACTION15D72 - 196
16X-RAY DIFFRACTION16D197 - 242
17X-RAY DIFFRACTION17D254 - 274
18X-RAY DIFFRACTION18E3 - 71
19X-RAY DIFFRACTION19E72 - 227
20X-RAY DIFFRACTION20E228 - 241
21X-RAY DIFFRACTION21E260 - 273
22X-RAY DIFFRACTION22F2 - 73
23X-RAY DIFFRACTION23F74 - 182
24X-RAY DIFFRACTION24F183 - 242
25X-RAY DIFFRACTION25F257 - 274

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