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- PDB-4u83: Structure of Brucella Abortus Butyryl-CoA dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4u83
TitleStructure of Brucella Abortus Butyryl-CoA dehydrogenase
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Butyryl-CoA dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Structure of Butyryl-CoA dehydrogenase from Brucella Abortus.
Authors: Fox III, D. / Horanyi, P.S. / Lorimer, D. / Edwards, T.E.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,37612
Polymers164,8794
Non-polymers4978
Water20,2311123
1
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8128
Polymers82,4402
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint5 kcal/mol
Surface area29370 Å2
MethodPISA
2
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5644
Polymers82,4402
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-8 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.970, 101.920, 95.910
Angle α, β, γ (deg.)90.000, 98.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-CoA dehydrogenase


Mass: 41219.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: A13334 / Gene: BAA13334_II01457 / Production host: Escherichia coli (E. coli) / References: UniProt: G8T5D9, EC: 1.3.99.2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1123 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: RigakuReagents MCSG-1 screen, G4: 0.1M Potassium Sodium Tartrate and 20% w/v PEG 3,350, cryo 20% EG; BrabA.00027.f.B1.PW37493 at 27.5mg/ml, tray 255764g4, puck uwi5-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 131545 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.102 / Χ2: 0.947 / Net I/σ(I): 11.38 / Num. measured all: 495552
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.850.8180.5092.7436603973897090.59499.7
1.85-1.90.8680.413.4435646946494440.47999.8
1.9-1.950.9020.3384.1134812925192300.39499.8
1.95-2.010.930.2814.8933768895989370.32899.8
2.01-2.080.9510.2226.0432684870486710.2699.6
2.08-2.150.9630.1916.9631534837783580.22499.8
2.15-2.230.9740.1558.3330513811480930.18199.7
2.23-2.320.9830.1289.8729101780177770.1599.7
2.32-2.430.9860.11210.8528273751874830.1399.5
2.43-2.550.9880.10111.8726710714871150.11899.5
2.55-2.680.9910.08613.6625752684368100.199.5
2.68-2.850.9930.07415.3324213640563830.08699.7
2.85-3.040.9940.06616.7323051609260730.07799.7
3.04-3.290.9940.05919.0621246564756250.06999.6
3.29-3.60.9950.05221.8619603520951810.06199.5
3.6-4.020.9950.04924.317660471847040.05799.7
4.02-4.650.9950.04425.915612417641670.05199.8
4.65-5.690.9960.04325.4213232353735280.0599.7
5.69-8.050.9960.0425.1710135275027410.04799.7
8.050.9970.03227.855404154515160.03898.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å48.2 Å
Translation1.8 Å48.2 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1760)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N5F
Resolution: 1.8→48.199 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 6533 4.97 %
Rwork0.1598 124969 -
obs0.1615 131502 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.24 Å2 / Biso mean: 18.7442 Å2 / Biso min: 5.58 Å2
Refinement stepCycle: final / Resolution: 1.8→48.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10965 0 32 1123 12120
Biso mean--34.43 28.22 -
Num. residues----1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811436
X-RAY DIFFRACTIONf_angle_d1.05215519
X-RAY DIFFRACTIONf_chiral_restr0.0421743
X-RAY DIFFRACTIONf_plane_restr0.0052061
X-RAY DIFFRACTIONf_dihedral_angle_d11.9134208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.27492210.229141864407100
1.8205-1.84190.25852130.212341344347100
1.8419-1.86430.24512280.200641394367100
1.8643-1.88790.26762260.194641774403100
1.8879-1.91280.24292250.191441184343100
1.9128-1.9390.22782120.189841444356100
1.939-1.96670.22722500.188741374387100
1.9667-1.9960.23222160.183341424358100
1.996-2.02720.23812270.175241884415100
2.0272-2.06050.19152240.170840974321100
2.0605-2.0960.21992350.162541294364100
2.096-2.13410.22332160.169841934409100
2.1341-2.17520.19762200.159741384358100
2.1752-2.21960.19622260.154941544380100
2.2196-2.26780.19672350.152741494384100
2.2678-2.32060.1981920.157541454337100
2.3206-2.37860.18392210.154441694390100
2.3786-2.44290.20591820.161841884370100
2.4429-2.51480.20752050.164841604365100
2.5148-2.5960.18882330.160941644397100
2.596-2.68870.192040.157441804384100
2.6887-2.79640.18561920.157741614353100
2.7964-2.92360.19062140.162341694383100
2.9236-3.07780.19682230.163541724395100
3.0778-3.27050.17892160.163541804396100
3.2705-3.5230.18022270.15941674394100
3.523-3.87740.17272320.14141644396100
3.8774-4.43810.15741920.129542294421100
4.4381-5.59020.1562070.138242234430100
5.5902-48.21640.16422190.15244273449299
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)
11.6010.6634-1.53681.1354-0.88521.78080.1215-0.25180.11690.0908-0.07950.1075-0.1133-0.0863-0.03950.17310.0166-0.01330.1766-0.0060.142822.6507-13.104850.0817
20.6904-0.0945-0.15750.5217-0.08970.9858-0.0001-0.1097-0.04770.0287-0.02860.02010.14140.10680.04190.12010.0337-0.00310.12280.02570.102334.5752-18.545839.911
30.6152-0.00680.24750.75380.1650.14-0.00240.0012-0.2026-0.02110.0225-0.09010.3740.2978-0.00630.26820.09780.01590.17610.00540.147841.9415-30.8728.883
40.9964-0.3149-0.17291.54790.11360.6885-0.06190.1213-0.1405-0.04470.0647-0.08140.29950.1874-0.00670.20650.0709-0.00490.1684-0.02270.10440.4293-28.569524.1515
50.38430.41710.09045.46060.66260.72220.0659-0.0552-0.00160.3013-0.0418-0.14450.00970.03350.00740.0891-0.00070.0060.130.01260.096224.4497-4.492636.5088
61.31670.40260.13572.41340.36880.74330.0182-0.07690.09050.0302-0.08650.1905-0.1055-0.0050.06110.1125-0.00050.0010.11930.00260.089115.9238-1.177537.6028
70.56680.23330.10651.8972-0.14860.7407-0.0066-0.03-0.02060.03460.00470.0133-0.01860.03980.00840.08530.01060.00420.11530.00490.083225.2823-4.627329.5157
86.22381.13461.91563.64730.5863.49820.03730.1282-0.3947-0.0437-0.02670.05570.1637-0.0487-0.03610.13510.01210.00280.0904-0.00260.126619.916-18.726221.0986
93.7888-1.89152.15491.8655-1.25362.31130.13670.27760.0075-0.317-0.11730.04550.1871-0.0052-0.00470.2398-0.00210.00320.16670.00340.151529.983213.6011-4.4375
101.08310.5894-0.11881.0857-0.15551.63330.0486-0.0035-0.117-0.0355-0.0958-0.15660.12380.28760.05520.10490.01510.00870.1590.01910.174545.697110.744910.6995
110.23120.14210.06791.14190.12090.99460.00890.04240.0603-0.08710.0041-0.0214-0.15520.05510.00540.108-0.01560.01030.11120.01870.118234.855323.19336.8164
120.951-0.11530.15131.44340.70131.5263-0.0201-0.00690.11540.09380.0364-0.1035-0.22480.1456-0.02470.1437-0.0371-0.01380.12820.0010.138241.79231.192320.6818
131.3203-0.54490.41222.15660.21111.107-0.0273-0.07230.18390.17960.0157-0.1376-0.0987-0.01970.00060.1716-0.03880.00270.1382-0.01140.113740.074131.571926.4884
140.53530.50510.27251.82030.29910.44770.0072-0.01120.08440.0501-0.0172-0.0786-0.09390.03420.01240.1513-0.01460.01110.14220.0010.134238.256928.38123.4594
150.6599-0.17940.04185.18651.88831.11870.01850.04550.0126-0.07370.0035-0.12050.01730.06610.01060.09020.0040.00280.12360.02290.072728.55764.50359.0292
160.79590.12920.05231.9634-0.05630.347-0.02660.0636-0.09830.0380.03430.16470.018-0.0016-0.00620.0951-0.0003-0.00280.1129-0.00450.097520.61530.655.2989
170.4179-0.2534-0.12171.5956-0.38040.5043-0.00480.03640.03610.0599-0.00430.0781-0.0439-0.0078-0.00650.0911-0.0094-0.01480.11970.00070.103220.987610.658314.0826
180.46870.2880.36391.9155-0.33271.1380.03240.0918-0.0402-0.1825-0.0517-0.14680.06170.19120.04630.10460.01170.01650.13070.01590.109733.7521-1.974117.1368
197.3702-2.5431-0.0613.130.2331.3307-0.12-0.19290.41970.19620.1150.0239-0.0634-0.17790.02920.1286-0.00110.00620.1111-0.00730.113118.433718.803322.1043
204.3229-0.12333.14011.36970.14384.19460.31480.0853-0.24560.181-0.0787-0.00970.5230.1737-0.27410.26390.00140.00370.1392-0.00080.189272.0781-23.818537.3879
211.264-0.0578-0.42252.189-0.54711.92440.04010.0618-0.0661-0.11110.00340.17030.2024-0.2029-0.03840.1311-0.0099-0.01970.1356-0.0130.155956.0899-13.154628.5211
221.2821-0.0459-0.29551.3753-0.00081.4647-0.0617-0.1585-0.07290.24350.01350.12090.07670.00420.05510.15240.00940.02290.13320.01730.142366.3219-16.269343.2519
231.0221-0.5685-0.62891.49880.83013.7678-0.0379-0.1249-0.10.2089-0.02420.06950.15810.05890.060.0959-0.01840.00990.12210.01290.123763.1222-6.966544.0391
241.2402-0.3134-0.13841.89430.34051.6299-0.0466-0.17940.06080.2065-0.05830.1963-0.1364-0.11950.10290.13950.01320.01040.1695-0.03490.14654.95041.757946.8327
250.831-0.64220.13450.9080.11152.1642-0.0139-0.03870.0685-0.0129-0.04310.1142-0.306-0.04520.07920.1682-0.00620.01490.1557-0.02920.165255.19097.320646.4197
260.8786-0.2568-0.31990.65640.72532.4745-0.0543-0.09370.06210.1095-0.1110.1075-0.1623-0.1640.16430.1459-0.00890.01320.1274-0.01390.148258.163.891643.7982
270.9405-0.3963-0.81451.41031.652.5985-00.0593-0.1363-0.0868-0.07620.1060.0086-0.14910.06340.09950.0001-0.01320.08140.0270.132375.5261-15.536222.6168
280.6748-0.166-1.16810.25850.83735.0543-0.0226-0.04660.01710.02520.0509-0.05340.07470.0502-0.05360.1126-0.0042-0.0180.11660.01070.157983.7018-14.081426.7631
290.36420.10940.04410.30740.1911.98080.0104-0.0062-0.0307-0.0010.0227-0.00530.0754-0.0467-0.04730.11620.0021-0.00080.08820.01390.126674.5177-6.52224.9195
306.53911.20831.30312.1170.37892.2917-0.01-0.4220.29050.0818-0.07480.0037-0.06670.05770.11470.12030.01450.00590.1153-0.01990.116879.48244.662738.0124
310.87190.2264-0.17431.3075-0.43371.2877-0.03190.03790.1434-0.02320.05770.0555-0.0667-0.0136-0.03340.13350.0195-0.01040.11690.0250.144169.470615.3302-1.8778
320.65270.0214-0.2891.55670.49281.3519-0.05150.1345-0.0171-0.17480.02680.0720.0753-0.10930.01770.1429-0.0153-0.03280.17360.0180.154666.4139-2.3744-12.5805
330.39960.25960.05140.68890.53121.7304-0.0390.0397-0.0331-0.06090.01710.04270.029-0.120.01790.10230.0065-0.01330.10130.02640.153669.0834-2.6185-4.7687
341.22290.3614-0.27190.8350.80436.5436-0.0221-0.13440.0470.1604-0.04130.050.06090.13240.05740.14130.01150.00140.090.0190.1683.875113.547313.1103
350.6206-0.038-0.52030.36060.08842.23840.05480.02670.0693-0.00090.00830.0036-0.115-0.0736-0.08910.09990.0033-0.0120.07220.01030.132376.02174.977812.5859
365.9661-1.1894-1.03412.33590.37772.7754-0.01350.4204-0.1671-0.0829-0.0162-0.07790.10120.11730.02520.1124-0.00080.00390.1011-0.01340.072685.2335-5.59641.7172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 21 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 101 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 162 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 236 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 266 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 305 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 358 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 359 through 375 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid -2 through 21 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 46 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 101 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 162 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 196 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 197 through 236 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 237 through 266 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 267 through 305 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 306 through 335 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 336 through 358 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 359 through 375 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid -1 through 21 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 22 through 45 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 46 through 77 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 78 through 101 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 102 through 162 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 163 through 196 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 197 through 236 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 237 through 272 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 273 through 305 )C0
29X-RAY DIFFRACTION29chain 'C' and (resid 306 through 358 )C0
30X-RAY DIFFRACTION30chain 'C' and (resid 359 through 375 )C0
31X-RAY DIFFRACTION31chain 'D' and (resid -1 through 77 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 78 through 162 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 163 through 266 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 267 through 305 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 306 through 358 )D0
36X-RAY DIFFRACTION36chain 'D' and (resid 359 through 375 )D0

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