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- PDB-8k04: CryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase Mh... -

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Basic information

Entry
Database: PDB / ID: 8k04
TitleCryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase MhpB in apo form
Components2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
KeywordsBIOSYNTHETIC PROTEIN / dioxygenase
Function / homology3-carboxyethylcatechol 2,3-dioxygenase / 3-carboxyethylcatechol 2,3-dioxygenase activity / 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / 3-phenylpropionate catabolic process / ferrous iron binding / 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the NADP-dependent malic enzyme in complex with oxaloacetate
Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
B: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
C: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
D: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
E: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
F: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
G: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
H: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
I: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
J: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase


Theoretical massNumber of molelcules
Total (without water)342,31010
Polymers342,31010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "I"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "A"
d_9ens_1chain "H"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 314 / Label seq-ID: 1 - 314

Dom-IDAuth asym-IDLabel asym-ID
d_1II
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8AA
d_9HH
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.808508235774, 0.588484708174, -0.000425359806766), (0.588484709384, -0.80850833542, -0.00013556219422), (-0.000423683227628, -0.000140714591782, -0.999999900346)-44.9542060212, 138.286012163, 225.608520029
2given(-0.307644442918, 0.951498548391, -0.00232575820088), (0.951500687407, 0.307646268614, 0.000463973656586), (0.00115698109293, -0.00207022160977, -0.999997187785)40.6997977644, -29.4378870861, 225.530092875
3given(-0.999999632509, -0.000857310542655, 5.13535288825E-7), (-0.000857310602994, 0.99999962379, -0.000132053879671), (-4.00323912387E-7, -0.000132054271402, -0.999999991281)226.750411017, 0.117807479847, 225.559790304
4given(-0.308929199831, -0.951084969515, -0.00036090768756), (-0.951084540193, 0.308929404142, -0.000905904303087), (0.000973086963353, 6.33934305994E-5, -0.999999524541)256.165010141, 186.247272719, 225.442740911
5given(-0.809004426024, 0.58780245047, 0.000343357453974), (-0.587802399697, -0.809004498878, 0.00024434904909), (0.000421406694813, -4.14687319108E-6, 0.9999999112)138.354444135, 271.608740465, -0.0472606961796
6given(-0.808972917699, -0.587845735804, 0.000457522536619), (0.587845813492, -0.808972989356, 4.52978482369E-5), (0.000343495227219, 0.000305597440184, 0.999999894311)271.572312901, 138.385310804, -0.0706498811306
7given(0.807121441518, -0.5903829212, 0.00172771431039), (-0.590381938567, -0.807123278012, -0.0010866023769), (0.00203598992313, -0.000142991247053, -0.999997917147)88.4628623179, 271.840926066, 225.327728411
8given(0.308974740648, -0.951070221461, 0.000208547924418), (0.9510702407, 0.308974712894, -0.000155071162904), (8.30475301732E-5, 0.000246256797014, 0.99999996623)186.072085514, -29.4462198005, -0.0373251156164
9given(0.309067049499, 0.951040247743, 7.80225454768E-5), (-0.951040227373, 0.309067022534, 0.000247992105085), (0.000211736277237, -0.000150848767608, 0.999999966206)-29.4980237987, 186.059069001, -0.0067230314217

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Components

#1: Protein
2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase / 3-carboxyethylcatechol 2 / 3-dioxygenase


Mass: 34230.961 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: mhpB, mhpB_1, A6592_08360, AAG43_003122, ACU57_18785, AM464_18695, AT845_003692, AW119_11075, BEA19_09385, BF481_002201, BG944_000993, BGM66_001457, BJI68_13680, BJJ90_20525, BKL28_002951, ...Gene: mhpB, mhpB_1, A6592_08360, AAG43_003122, ACU57_18785, AM464_18695, AT845_003692, AW119_11075, BEA19_09385, BF481_002201, BG944_000993, BGM66_001457, BJI68_13680, BJJ90_20525, BKL28_002951, BLM69_004076, BMC79_001945, BMT50_03125, BMT91_19310, BON92_03390, BTB68_001828, BUO55_000492, BvCmsKKP061_02674, BXT93_09690, BZL69_13825, C0P57_002705, C2R31_002140, C3F40_10810, C5N07_24670, C9E67_23975, CA593_01390, CDL36_14360, CDL37_09265, CG831_000406, CIG67_02690, CQ986_000779, CV83915_01226, CX938_004022, D0X26_07210, D4M65_16025, D9H94_11950, DN627_27135, DTL43_07625, DTL90_10525, DTM45_10750, DU321_19275, E4K51_23600, E5H86_16710, E6D34_13465, EA435_05985, EAN77_08135, EAX79_07015, EBP16_14625, ECs0403, EIZ93_16195, EL79_3496, ELT17_10045, ELT48_00575, ELX68_17755, ELX76_06030, ELX79_17290, EPS76_18260, ERS139208_01777, ExPECSC038_04860, F7F11_06665, F9413_17095, F9461_15720, F9S83_01345, FDM60_22665, FJQ53_15090, FKO60_15565, FOI11_011700, FOI11_08345, FPI65_01895, FV293_06300, FVB16_14265, FWK02_24950, FZU14_00995, G3565_02695, G3V95_15725, G4A38_05225, G4A47_03610, GF699_21980, GFY34_04780, GIB53_19760, GJ11_02180, GJO56_07880, GKF66_16190, GKF89_21475, GNW61_15375, GOP25_04445, GP944_04070, GP965_12675, GQM13_16935, GQM21_19370, GRC73_20955, GRW05_10415, GRW57_19650, GSM54_06355, GUI33_03835, H0O72_17150, HEP30_020365, HHH44_001337, HI055_001759, HIE29_000752, HJQ60_002399, HKA49_003062, HLV18_07550, HLX92_10820, HLZ50_17845, HMV95_12485, HV109_18305, HVY77_20140, HVZ29_04840, HX136_19710, IH772_19545, J4S20_003623, J5U05_003482, NCTC10418_05740, NCTC10429_03811, NCTC10764_05415, NCTC10974_04398, NCTC11126_05668, NCTC12950_04217, NCTC13127_05199, NCTC13148_06746, NCTC13216_02859, NCTC8179_01606, NCTC8333_04573, NCTC8450_01327, NCTC8622_02936, NCTC9044_03463, NCTC9045_04477, NCTC9073_03083, NCTC9077_04839, NCTC9111_04016, NCTC9962_02508, ND22_001410, SAMEA3472044_00503, SAMEA3472056_02987, SAMEA3751407_04552, SAMEA3752557_00177, SAMEA3753106_00568, WR15_20705
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C3TMW2, 3-carboxyethylcatechol 2,3-dioxygenase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364814 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 161.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010924740
ELECTRON MICROSCOPYf_angle_d0.742933650
ELECTRON MICROSCOPYf_chiral_restr0.04673680
ELECTRON MICROSCOPYf_plane_restr0.00464460
ELECTRON MICROSCOPYf_dihedral_angle_d5.06223380
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2IIELECTRON MICROSCOPYNCS constraints0.000708921267193
ens_1d_3IIELECTRON MICROSCOPYNCS constraints0.000699238984342
ens_1d_4IIELECTRON MICROSCOPYNCS constraints0.000715794740102
ens_1d_5IIELECTRON MICROSCOPYNCS constraints0.0742115612656
ens_1d_6IIELECTRON MICROSCOPYNCS constraints0.00070869891733
ens_1d_7IIELECTRON MICROSCOPYNCS constraints0.0742149278015
ens_1d_8IIELECTRON MICROSCOPYNCS constraints0.000707948234127
ens_1d_9IIELECTRON MICROSCOPYNCS constraints0.000701542354302
ens_1d_10IIELECTRON MICROSCOPYNCS constraints0.00070690614069

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