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- PDB-5tjr: X-ray Crystal structure of a methylmalonate semialdehyde dehydrog... -

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Basic information

Entry
Database: PDB / ID: 5tjr
TitleX-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC
ComponentsMethylmalonate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / industrial biotechnology / hexamer
Function / homology
Function and homology information


methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / nucleotide binding
Similarity search - Function
Methylmalonate-semialdehyde dehydrogenase / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Methylmalonate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. AAC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPeat, T.S. / Newman, J.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida.
Authors: Tararina, M.A. / Janda, K.D. / Allen, K.N.
History
DepositionOct 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonate-semialdehyde dehydrogenase
B: Methylmalonate-semialdehyde dehydrogenase
C: Methylmalonate-semialdehyde dehydrogenase
D: Methylmalonate-semialdehyde dehydrogenase
E: Methylmalonate-semialdehyde dehydrogenase
F: Methylmalonate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,20111
Polymers344,0656
Non-polymers2,1365
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28140 Å2
ΔGint-61 kcal/mol
Surface area103060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.891, 156.631, 192.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A34 - 527
2010B34 - 527
1020A35 - 527
2020C35 - 527
1030A35 - 527
2030D35 - 527
1040A35 - 527
2040E35 - 527
1050A34 - 527
2050F34 - 527
1060B35 - 527
2060C35 - 527
1070B35 - 527
2070D35 - 527
1080B35 - 527
2080E35 - 527
1090B34 - 527
2090F34 - 527
10100C35 - 527
20100D35 - 527
10110C35 - 527
20110E35 - 527
10120C35 - 527
20120F35 - 527
10130D35 - 527
20130E35 - 527
10140D35 - 527
20140F35 - 527
10150E35 - 527
20150F35 - 527

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Methylmalonate-semialdehyde dehydrogenase


Mass: 57344.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. AAC (bacteria) / Gene: FG99_15390 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A081YAY7
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.54 Å3/Da / Density % sol: 51.49 % / Description: rhombohedral crystals
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Protein at 5 mg/mL with added acetyl-CoA; crystal conditions were 100 mM bis-tris propane at pH 7.6, 24% PEG 3350, 210 mM trisodium citr ate in 150 plus 150 nL drops.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.95→49.6 Å / Num. obs: 74332 / % possible obs: 99.9 % / Redundancy: 14.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.178 / Net I/σ(I): 11.5
Reflection shellResolution: 2.95→3.01 Å / Redundancy: 15 % / Rmerge(I) obs: 1.607 / Mean I/σ(I) obs: 2 / CC1/2: 0.818 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zz7

4zz7


Resolution: 2.95→49 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.929 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24862 3714 5 %RANDOM
Rwork0.21236 ---
obs0.21417 70516 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.029 Å2
Baniso -1Baniso -2Baniso -3
1--4.13 Å2-0 Å20 Å2
2--7.93 Å20 Å2
3----3.8 Å2
Refinement stepCycle: 1 / Resolution: 2.95→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20813 0 135 16 20964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01921403
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220444
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9729099
X-RAY DIFFRACTIONr_angle_other_deg1.058346919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98452741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03523.993894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.191153356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7315133
X-RAY DIFFRACTIONr_chiral_restr0.1060.23278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02124386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1717.02111033
X-RAY DIFFRACTIONr_mcbond_other5.1667.02111032
X-RAY DIFFRACTIONr_mcangle_it8.04210.52313751
X-RAY DIFFRACTIONr_mcangle_other8.04310.52313752
X-RAY DIFFRACTIONr_scbond_it5.3067.52610370
X-RAY DIFFRACTIONr_scbond_other5.3067.52610371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.65611.06315349
X-RAY DIFFRACTIONr_long_range_B_refined14.27486950
X-RAY DIFFRACTIONr_long_range_B_other14.27486951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A270120.11
12B270120.11
21A266780.12
22C266780.12
31A267680.11
32D267680.11
41A268840.11
42E268840.11
51A268720.11
52F268720.11
61B265200.12
62C265200.12
71B272180.11
72D272180.11
81B267680.11
82E267680.11
91B268240.11
92F268240.11
101C263280.12
102D263280.12
111C263900.11
112E263900.11
121C264060.12
122F264060.12
131D263800.11
132E263800.11
141D265560.11
142F265560.11
151E267200.11
152F267200.11
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 268 -
Rwork0.356 5126 -
obs--99.96 %

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