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- PDB-8ih7: AmnG-AmnH complex -

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Basic information

Entry
Database: PDB / ID: 8ih7
TitleAmnG-AmnH complex
Components
  • 4-hydroxy-2-oxovalerate aldolase
  • Acetaldehyde dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / meta-cleavage pathway for 2-aminophenol catabolism. Aldolase for 4-hydroxy-2-oxovalerate. Acetaldehyde dehydrogenase
Function / homology
Function and homology information


4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase activity / acetaldehyde dehydrogenase (acetylating) / : / acetaldehyde dehydrogenase (acetylating) activity / NAD binding / manganese ion binding
Similarity search - Function
DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain ...DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
OXALATE ION / 4-hydroxy-2-oxovalerate aldolase / Acetaldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSu, D. / Shi, Q.L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0505903 China
CitationJournal: To Be Published
Title: AmnG-AmnH complex
Authors: Su, D. / Shi, Q.L.
History
DepositionFeb 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-2-oxovalerate aldolase
B: Acetaldehyde dehydrogenase
C: 4-hydroxy-2-oxovalerate aldolase
D: Acetaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6428
Polymers144,3354
Non-polymers3074
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-112 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.029, 252.288, 60.785
Angle α, β, γ (deg.)90.00, 114.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 4-hydroxy-2-oxovalerate aldolase / HOA / 4-hydroxy-2-keto-pentanoic acid aldolase / 4-hydroxy-2-oxopentanoate aldolase


Mass: 38551.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnG / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9KWS0, 4-hydroxy-2-oxovalerate aldolase
#2: Protein Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase [acetylating]


Mass: 33615.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnH / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KWS1, acetaldehyde dehydrogenase (acetylating)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.2M magnesium chloride hexahydrate,0.2 M Tris 8.5,20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.48→63.07 Å / Num. obs: 52921 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 14.2
Reflection shellResolution: 2.48→2.55 Å / Num. unique obs: 52921 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→20.11 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 1996 3.79 %
Rwork0.173 --
obs0.1749 52734 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→20.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9743 0 14 300 10057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.937
X-RAY DIFFRACTIONf_dihedral_angle_d6.1361400
X-RAY DIFFRACTIONf_chiral_restr0.0551551
X-RAY DIFFRACTIONf_plane_restr0.0081759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.540.29991380.25223618X-RAY DIFFRACTION100
2.54-2.610.27531530.23043632X-RAY DIFFRACTION100
2.61-2.690.28721300.22943585X-RAY DIFFRACTION100
2.69-2.770.32041530.22953652X-RAY DIFFRACTION100
2.77-2.870.30391370.21963609X-RAY DIFFRACTION100
2.87-2.990.311430.21653608X-RAY DIFFRACTION100
2.99-3.120.27831360.22153625X-RAY DIFFRACTION100
3.12-3.290.28541460.21373606X-RAY DIFFRACTION100
3.29-3.490.23071480.19993631X-RAY DIFFRACTION100
3.49-3.760.22551400.17573632X-RAY DIFFRACTION100
3.76-4.140.20471380.15373623X-RAY DIFFRACTION100
4.14-4.730.18531460.12943622X-RAY DIFFRACTION100
4.73-5.930.16951460.1363629X-RAY DIFFRACTION100
5.93-20.110.15291420.13013666X-RAY DIFFRACTION100
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)
10.12470.0952-0.32970.6763-0.30330.5163-0.0489-0.05730.05930.21950.07070.026-0.0944-0.0064-00.39560.0392-0.05580.4627-0.0980.401315.388497.795161.8465
20.08320.1360.07080.1563-0.0020.138-0.1883-0.2958-0.02450.23920.1702-0.05380.22870.11330.00020.39320.0121-0.03930.5326-0.02040.290810.563287.644165.0171
30.3837-0.0149-0.05991.0947-0.18320.1857-0.04320.01850.0681-0.13010.0212-0.0049-0.0024-0.031-00.31340.0045-0.02920.396-0.07150.397712.819696.467148.0452
4-0.00820.0260.10170.0060.10840.2744-0.018-0.15920.2149-0.37080.1388-0.02030.2150.06520.00020.54440.010.05730.4868-0.03090.33320.414147.715838.1891
50.16120.04940.18990.13230.17040.2094-0.02080.3845-0.4201-0.23790.04340.60270.3868-0.6846-0.00010.6101-0.1056-0.05290.6637-0.05930.43775.835148.810739.3758
60.1716-0.009-0.12730.35690.0930.39940.0124-0.08430.04670.2406-0.096-0.28260.26160.0392-00.4673-0.01260.01640.39080.02380.312518.459752.395453.7969
70.2288-0.22240.03251.32270.1840.6871-0.0045-0.1651-0.0188-0.0297-0.0389-0.11140.0725-0.07500.3616-0.0002-0.0240.4420.02930.356526.163173.595451.9083
80.0190.04760.050.04330.0110.0281-0.18070.3844-0.4796-0.05580.2828-0.65510.33240.516-0.00060.39650.0280.06490.5022-0.0190.618140.090166.976545.7295
90.4971-0.08720.16980.6259-0.02650.0305-0.05040.01930.0107-0.1920.079-0.38720.03550.0536-00.3703-0.00970.00660.4334-0.00950.393232.766577.56848.2349
100.09310.0359-0.00840.11430.11640.0603-0.16830.1105-0.1383-0.24260.0411-0.01670.1779-0.0924-0.00010.50210.03630.03950.4501-0.00920.4424.889753.10746.5222
110.1596-0.1530.15880.5178-0.48290.2276-0.06210.13320.1484-0.31020.0563-0.3648-0.05440.0528-00.4739-0.03250.0690.4735-0.10870.634325.7173125.425732.706
120.2307-0.17640.16711.54720.01870.2072-0.01870.02340.0269-0.15590.0965-0.14-0.05530.009300.423-0.02940.00950.394-0.09840.477914.1458125.687537.8863
131.10130.0218-0.51060.8919-0.17261.113-0.17710.2062-0.1404-0.08260.28220.06830.2311-0.4796-0.00010.5368-0.05210.04030.5710.00720.34231.475170.071637.5897
14-0.1817-0.75990.0441.9844-0.12980.6265-0.01520.01220.17790.10950.1414-0.422-0.0705-0.04810.00490.4947-0.02060.00840.4586-0.15080.64919.0188153.589147.8949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 338 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 37 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 67 )
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 130 )
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 219 )
8X-RAY DIFFRACTION8chain 'B' and (resid 220 through 237 )
9X-RAY DIFFRACTION9chain 'B' and (resid 238 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 289 through 314 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 78 )
12X-RAY DIFFRACTION12chain 'C' and (resid 79 through 338 )
13X-RAY DIFFRACTION13chain 'D' and (resid -1 through 112 )
14X-RAY DIFFRACTION14chain 'D' and (resid 113 through 309 )

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