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- PDB-4eye: Crystal structure of a probable oxidoreductase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4eye
TitleCrystal structure of a probable oxidoreductase from Mycobacterium abscessus solved by iodide ion SAD
ComponentsProbable oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / FadB4 ortholog / virulence
Function / homology
Function and homology information


oxidoreductase activity / zinc ion binding
Similarity search - Function
: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain ...: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Probable oxidoreductase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsEdwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Probable oxidoreductase
B: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,17122
Polymers71,6502
Non-polymers2,52120
Water5,116284
1
A: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33913
Polymers35,8251
Non-polymers1,51412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8329
Polymers35,8251
Non-polymers1,0078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.640, 46.340, 84.130
Angle α, β, γ (deg.)90.000, 93.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: -1 - 321 / Label seq-ID: 20 - 342

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable oxidoreductase


Mass: 35825.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_4603c / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B1ML27
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyabA.01189.a.A1 PS00933 at 28 mg/mL supplemented with 0.5 M KI against Morpheus screen condition D4, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.1 M MES/imidazole pH 6.5, 0.02 M alcohols, ...Details: MyabA.01189.a.A1 PS00933 at 28 mg/mL supplemented with 0.5 M KI against Morpheus screen condition D4, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.1 M MES/imidazole pH 6.5, 0.02 M alcohols, crystal tracking ID 233762d4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 254775 / Rmerge(I) obs: 0.06 / D res high: 2.1 Å / Num. obs: 68977 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.649.39142499.910.029
5.426.64184799.910.033
4.75.42212899.810.034
4.24.7241898.410.034
3.834.227119910.037
3.553.83293799.510.038
3.323.55318899.710.042
3.133.32335099.610.049
2.973.13360299.910.059
2.832.97374399.910.07
2.712.83391299.610.085
2.62.71409499.910.102
2.512.6434299.710.137
2.422.51434299.610.165
2.352.42453899.810.193
2.282.35472099.810.239
2.212.28483699.610.274
2.152.21502999.710.322
2.12.15506299.810.433
ReflectionResolution: 2.1→50 Å / Num. all: 35785 / Num. obs: 35731 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 36.245 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.46
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.4741831025981100
2.15-2.210.355.351837425781100
2.21-2.280.2976.24176622483199.8
2.28-2.350.2617.15174082419199.9
2.35-2.420.2128.611682523331100
2.42-2.510.1839.94160712233199.9
2.51-2.60.15311.49161702237199.9
2.6-2.710.11614.681526921081100
2.71-2.830.09816.94146082018199.9
2.83-2.970.08219.651395819301100
2.97-3.130.0722.421347818621100
3.13-3.320.05926.28124331739199.9
3.32-3.550.0529.61175016561100
3.55-3.830.04632.04107681534199.9
3.83-4.20.04633.6597461418199.3
4.2-4.70.04334.7184421274198.8
4.7-5.420.04634.98793811241100
5.42-6.640.0535.0170009831100
6.64-9.390.04437.1754137711100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 42 Å / FOM : 0.334 / FOM acentric: 0.348 / FOM centric: 0.134 / Reflection: 35647 / Reflection acentric: 33229 / Reflection centric: 2249
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.41-10.20.3990.4620.11626021148
7.32-8.410.4750.5320.15530125546
6.57-7.320.4830.5250.19632628442
6.01-6.570.4860.5360.1836731650
5.57-6.010.5080.550.19841336449
5.22-5.570.4750.5080.20842137545
4.92-5.220.4680.5030.12946041743
4.67-4.920.4540.4940.12946541547
4.46-4.670.3980.4340.151045645
4.27-4.460.4350.470.1151746843
4.1-4.270.3960.4330.07154448948
3.96-4.10.4090.4340.12253949638
3.82-3.960.4170.4450.10957052242
3.7-3.820.4160.4470.10461355650
3.59-3.70.4250.4520.08261457042
3.49-3.590.4160.4450.08463758747
3.4-3.490.4270.4520.11465660944
3.31-3.40.4120.4410.0864959845
3.23-3.310.4070.4330.09670665248
3.16-3.230.4020.4210.14971266345
3.09-3.160.4060.4260.16767562349
3.03-3.090.4050.4210.1275371438
2.97-3.030.4040.4250.11475570450
2.91-2.970.3960.4110.12373669640
2.85-2.910.3890.4070.12379574351
2.8-2.850.3730.3870.11879375238
2.75-2.80.3880.4050.14779974747
2.71-2.750.3690.3810.18380575744
2.66-2.710.3570.370.1486181049
2.62-2.660.3490.360.12383779839
2.58-2.620.3250.3380.12883978649
2.55-2.580.3250.3330.1786382437
2.51-2.550.3090.320.14291686049
2.47-2.510.3020.3120.08887182839
2.44-2.470.2870.2950.14690985650
2.41-2.440.2880.2970.1492086844
2.38-2.410.2720.2780.16694489348
2.35-2.380.2640.270.15991586744
2.32-2.350.2530.260.10794890342
2.29-2.320.2450.250.14797492846
2.26-2.290.2320.2380.11799294444
2.24-2.260.2390.2430.17997091944
2.21-2.240.2250.2280.155100895747
2.19-2.210.2170.220.142100996740
2.17-2.190.2120.2160.134102296648
2.14-2.170.2060.210.128104599247
2.12-2.140.2030.2060.10399495040
2.1-2.120.1950.1980.151073102247

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2326 / WRfactor Rwork: 0.1841 / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8703 / SU B: 7.68 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2232 / SU Rfree: 0.1876 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1790 5 %RANDOM
Rwork0.185 ---
obs0.1875 35731 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.25 Å2 / Biso mean: 32.9471 Å2 / Biso min: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.2 Å2
2---0.05 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 34 284 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194530
X-RAY DIFFRACTIONr_bond_other_d0.0040.022925
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9816181
X-RAY DIFFRACTIONr_angle_other_deg1.09637157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83223.654156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52915642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1061527
X-RAY DIFFRACTIONr_chiral_restr0.090.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215173
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02882
Refine LS restraints NCS

Ens-ID: 1 / Number: 9340 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.08 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 106 -
Rwork0.22 2366 -
all-2472 -
obs--99.96 %
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)
10.1304-0.0148-0.02350.84970.05390.77280.01980.06290.039-0.0118-0.0537-0.0343-0.0439-0.03460.03390.1594-0.01050.00940.16010.0110.192668.308124.01677.5284
20.8567-0.350.24330.16310.01290.7921-0.0414-0.0812-0.00060.03290.03520.01810.08450.06240.00610.2096-0.01920.0020.17480.00370.151781.21827.034323.2523
30.43172.6699-1.144916.8318-7.19263.07610.4108-0.0444-0.00492.1114-0.5244-0.217-0.93230.22720.11360.6502-0.02180.09170.46880.18350.1394.151414.917733.4793
40.6092-0.4056-0.01130.5171-0.15610.5091-0.0576-0.02740.0010.0681-0.00320.013-0.02870.0520.06080.1732-0.03440.00150.1508-0.00450.156778.711812.684617.9517
51.22540.7054-0.25890.4174-0.23040.90070.082-0.2346-0.05560.0585-0.1149-0.01550.067-0.12510.03280.2059-0.04590.03750.1540.00310.174851.58846.155435.9353
62.3285-0.26850.37250.4008-0.20840.1473-0.21740.48240.11030.03020.1649-0.10150.0095-0.04770.05240.1776-0.1286-0.02370.29290.01760.163740.026910.88614.9849
75.6136-1.289-0.46242.08730.43690.1045-0.37670.44750.74320.61790.29290.37310.11010.05730.08380.2653-0.04020.00630.33580.28170.43625.481219.263912.6935
82.03040.38040.34180.1784-0.07790.3548-0.1032-0.02320.0042-0.04150.0857-0.0222-0.0146-0.02920.01750.1715-0.06550.01580.1609-0.01460.151143.65758.961622.755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 98
2X-RAY DIFFRACTION2A99 - 215
3X-RAY DIFFRACTION3A218 - 224
4X-RAY DIFFRACTION4A225 - 321
5X-RAY DIFFRACTION5B-1 - 98
6X-RAY DIFFRACTION6B99 - 198
7X-RAY DIFFRACTION7B199 - 252
8X-RAY DIFFRACTION8B253 - 321

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