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- PDB-3pfd: Crystal structure of an Acyl-CoA dehydrogenase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 3pfd
TitleCrystal structure of an Acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to reduced flavin adenine dinucleotide solved by combined iodide ion SAD MR
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dehydrogenase / de novo phase determination / iodide ion SAD / acyl coA dehydrogenase / reduced flavin adenine dinucleotide / FAD / fatty acid metabolism
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / 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 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / 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 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / IODIDE ION / Probable acyl-CoA dehydrogenase fadE25
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SAD WITH molecular replacement / SAD / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J.STRUCT.FUNCT.GENOM. / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)185,257117
Polymers168,2744
Non-polymers16,983113
Water11,223623
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,79033
Polymers42,0691
Non-polymers4,72232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,40930
Polymers42,0691
Non-polymers4,34129
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,64824
Polymers42,0691
Non-polymers3,57923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,40930
Polymers42,0691
Non-polymers4,34129
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.430, 114.550, 92.770
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A18 - 389
2116B18 - 389
3116C18 - 389
4116D18 - 389

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Components

#1: Protein
Acyl-CoA dehydrogenase


Mass: 42068.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / NCTC 10409 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CNE7*PLUS, EC: 1.3.99.3
#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 109 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: MythA00185bA1 PS00649 116 mg/mL grown against JCSG+ C1 0.2 M NaCl, 0.1 M phosphate citrate pH 4.2, 20% PEG 8000 and soaked for 20 minutes against 15% PEG 8000, 25% PEG 400, 1 M NaI, 0.1 M ...Details: MythA00185bA1 PS00649 116 mg/mL grown against JCSG+ C1 0.2 M NaCl, 0.1 M phosphate citrate pH 4.2, 20% PEG 8000 and soaked for 20 minutes against 15% PEG 8000, 25% PEG 400, 1 M NaI, 0.1 M phosphate citrate pH 4.2, crystal tracking ID 216661c1-1MNaI, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 650541 / Rmerge(I) obs: 0.11 / D res high: 2.1 Å / Num. obs: 177142 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.649.39364899.810.038
5.426.64473910010.054
4.75.42559610010.048
4.24.7634110010.044
3.834.2705999.810.047
3.553.83758599.810.057
3.323.55825399.810.07
3.133.32867599.910.085
2.973.13922699.910.113
2.832.97973499.910.137
2.712.831016899.810.164
2.62.711060499.910.179
2.512.61099099.910.219
2.422.511141699.910.258
2.352.421171399.810.277
2.282.351218699.810.308
2.212.281252599.810.335
2.152.211282299.810.403
2.12.151193589.810.476
ReflectionResolution: 2.1→50 Å / Num. obs: 89991 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.921 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.1-2.156.20.5313.5376686704611491.2
2.15-2.210.4434.4457926488100
2.21-2.280.3715.2451886336100
2.28-2.350.345.6441156164100
2.35-2.420.3086.2427135926100
2.42-2.510.2866.5418735779100
2.51-2.60.2457.5404085561100
2.6-2.710.2018.8392415370100
2.71-2.830.1869.4378535152100
2.83-2.970.15610.9364664932100
2.97-3.130.13212.6347264679100
3.13-3.320.115.9327624405100
3.32-3.550.08318.9312334196100
3.55-3.830.07122287553857100
3.83-4.20.06225267813599100
4.2-4.70.06125.8240843235100
4.7-5.420.07324.4213312857100
5.42-6.640.08822.1180852432100
6.64-9.390.06427.8137961890100
9.390.065307018101996.5

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 29.47 Å / FOM : 0.525 / FOM acentric: 0.529 / FOM centric: 0.395 / Reflection: 89868 / Reflection acentric: 87142 / Reflection centric: 2307
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.91-13.290.7870.8090.56451847048
8.25-9.910.7720.7780.69664159146
7.22-8.250.7450.7520.63675570549
6.49-7.220.7080.7140.59884879948
5.95-6.490.710.7190.53892888345
5.53-5.950.6930.7040.483100695749
5.18-5.530.6760.6890.3771056100947
4.89-5.180.6620.6760.3271140109346
4.65-4.890.6790.6860.4881184113944
4.44-4.650.6620.6720.4111286123451
4.25-4.440.6440.650.5031305125747
4.09-4.250.6470.6560.4331349129749
3.94-4.090.6140.6220.3921419137243
3.81-3.940.6210.6290.41480142351
3.69-3.810.620.6290.3691497144150
3.58-3.690.5920.60.3021575152643
3.48-3.580.5710.580.3041620156652
3.39-3.480.5550.5590.3941647159742
3.31-3.390.5610.5670.3781686163349
3.23-3.310.5530.5580.3691743169246
3.16-3.230.5580.5660.2681791173947
3.09-3.160.5520.5580.3031785173644
3.02-3.090.5610.5650.3721858181146
2.96-3.020.5440.5490.371918186551
2.91-2.960.5360.5410.3291930188245
2.85-2.910.5250.530.3511963191446
2.8-2.850.520.5230.3962036197854
2.75-2.80.5260.5280.462015197440
2.71-2.750.510.5140.3542085202748
2.66-2.710.5030.5070.332094205139
2.62-2.660.5110.5160.3322143208156
2.58-2.620.5080.510.3492156211338
2.54-2.580.50.5020.3722218216251
2.51-2.540.4810.4840.3442244220238
2.47-2.510.4810.4850.3362266220951
2.44-2.470.4870.490.3562286223443
2.41-2.440.4740.4780.3062340228846
2.38-2.410.4760.4790.342345229347
2.35-2.380.460.4610.4462416236442
2.32-2.350.4630.4650.3632410235843
2.29-2.320.4620.4640.3982484243344
2.26-2.290.4570.4590.3272471242043
2.24-2.260.4420.4440.3562502243853
2.21-2.240.4450.4480.3382547249541
2.19-2.210.4360.4380.322559250247
2.17-2.190.4230.4260.3072584252547
2.14-2.170.4190.4210.3132632255848
2.12-2.140.4220.4230.4512409229440
2.1-2.120.4330.4370.3162353221837

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: SAD WITH molecular replacement
Starting model: 1jqi

1jqi


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.1863 / WRfactor Rwork: 0.1541 / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8883 / SU B: 7.088 / SU ML: 0.106 / SU R Cruickshank DPI: 0.2022 / SU Rfree: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 4507 5 %RANDOM
Rwork0.1691 ---
obs0.171 89872 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.4 Å2 / Biso mean: 21.3214 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.36 Å2
2---0.09 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10870 0 321 623 11814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211292
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.98315327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34651472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86623.87447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.581151797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5611579
X-RAY DIFFRACTIONr_chiral_restr0.0920.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218483
X-RAY DIFFRACTIONr_mcbond_it0.6641.57291
X-RAY DIFFRACTIONr_mcangle_it1.17211553
X-RAY DIFFRACTIONr_scbond_it2.03334001
X-RAY DIFFRACTIONr_scangle_it3.2624.53771
Refine LS restraints NCS

Ens-ID: 1 / Number: 2652 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.215
2BLOOSE POSITIONAL0.265
3CLOOSE POSITIONAL0.255
4DLOOSE POSITIONAL0.225
1ALOOSE THERMAL2.5510
2BLOOSE THERMAL1.7710
3CLOOSE THERMAL3.2510
4DLOOSE THERMAL2.1410
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 302 -
Rwork0.194 5793 -
all-6095 -
obs--91.11 %
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)
10.42350.03720.06880.49770.31360.5135-0.0196-0.0688-0.05780.041-0.03220.03220.0039-0.0330.05190.0818-0.00960.02950.089-0.00670.081426.744936.066945.2642
20.3679-0.0939-0.14680.78260.13070.43250.04340.01780.0380.0032-0.0320.0362-0.0855-0.0392-0.01130.09930.02010.01530.0407-0.01540.096624.735356.452533.9277
30.10070.1021-0.05720.87930.4010.3520.0435-0.0364-0.00350.04-0.0535-0.04180.0267-0.01860.010.1-0.0061-0.00480.08880.00070.078941.140124.497436.7035
40.36250.29460.00310.26940.03070.121-0.0117-0.02390.0271-0.02710.0119-0.00010.0045-0.009-0.00020.07830.0039-0.00590.0833-0.00270.102539.435435.264630.6985
50.05380.10590.05710.32920.11010.73360.00010.02640.0236-0.0539-0.01440.02180.1178-0.05240.01430.10530.003-0.01790.1078-0.00670.058728.86715.00943.4127
60.48560.16420.03861.39580.29830.52740.05810.01030.05410.0014-0.04710.03010.2183-0.1536-0.0110.1677-0.0658-0.0290.0576-0.0080.03825.19011.200113.0992
70.0568-0.0639-0.00380.44230.42130.4990.060.06370.0378-0.0343-0.0817-0.0652-0.0027-0.02620.02170.08240.03150.00980.11440.02210.093942.513235.534110.3357
80.3795-0.3569-0.03870.61960.06160.12820.02510.05980.00970.0025-0.0408-0.02330.0326-0.03670.01570.0857-0.0022-0.00930.0879-0.00690.085540.242522.871916.0397
90.66550.01770.02880.3402-0.1180.32580.02560.2224-0.0506-0.0002-0.0522-0.03820.03120.12680.02660.03080.04550.03040.17970.01970.04674.635929.22630.7056
100.92380.1230.13730.7808-0.4480.963-0.00680.14830.1403-0.0292-0.048-0.10790.00320.14250.05480.01210.00950.02510.14190.10810.124277.584945.93350.4392
110.2406-0.17970.14290.1492-0.18550.73430.08790.0577-0.0547-0.0458-0.02850.04260.06730.0418-0.05940.09280.0165-0.01460.0821-0.00970.097260.363416.413917.484
120.3108-0.26580.24930.2883-0.14680.4380.01810.0747-0.02220.0014-0.0272-0.0058-0.00460.05050.00920.06590.00750.00410.10950.01360.095762.097330.050114.2417
130.9865-0.0582-0.5270.2707-0.15861.2053-0.0606-0.02690.12830.12750.0454-0.0973-0.04820.02430.01530.0772-0.005-0.04940.0566-0.01690.111973.082637.814547.4035
140.4561-0.28780.11640.744-0.42230.2983-0.0613-0.0089-0.02870.0820.0382-0.0796-0.01960.01970.02310.07580.0301-0.03740.07540.01160.094775.384815.314349.848
150.08590.0121-0.07890.2564-0.38131.0110.0194-0.01750.08870.03350.01650.003-0.00240.0339-0.03590.0675-0.0075-0.0080.0820.00720.116459.642440.704532.4224
160.30290.2336-0.12850.2524-0.10850.24630.0147-0.02420.04140.01520.0022-0.00730.05350.0365-0.01690.07130.0067-0.01560.08420.01020.110161.203728.44434.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 98
2X-RAY DIFFRACTION2A99 - 246
3X-RAY DIFFRACTION3A247 - 313
4X-RAY DIFFRACTION4A314 - 389
5X-RAY DIFFRACTION5B18 - 149
6X-RAY DIFFRACTION6B150 - 251
7X-RAY DIFFRACTION7B252 - 313
8X-RAY DIFFRACTION8B314 - 389
9X-RAY DIFFRACTION9C19 - 149
10X-RAY DIFFRACTION10C150 - 251
11X-RAY DIFFRACTION11C252 - 313
12X-RAY DIFFRACTION12C314 - 389
13X-RAY DIFFRACTION13D18 - 88
14X-RAY DIFFRACTION14D89 - 246
15X-RAY DIFFRACTION15D247 - 313
16X-RAY DIFFRACTION16D314 - 389

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