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- PDB-8abu: Crystal structure of NaLdpA mutant H97Q in complex with erythro-DGPD -

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Basic information

Entry
Database: PDB / ID: 8abu
TitleCrystal structure of NaLdpA mutant H97Q in complex with erythro-DGPD
ComponentsSnoaL-like domain-containing protein
KeywordsLYASE / lignin / dehydratase
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Chem-LJU / SnoaL-like domain-containing protein
Function and homology information
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.661 Å
AuthorsZahn, M. / Kuatsjah, E. / Beckham, G.T. / McGeehan, J.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation.
Authors: Kuatsjah, E. / Zahn, M. / Chen, X. / Kato, R. / Hinchen, D.J. / Konev, M.O. / Katahira, R. / Orr, C. / Wagner, A. / Zou, Y. / Haugen, S.J. / Ramirez, K.J. / Michener, J.K. / Pickford, A.R. / ...Authors: Kuatsjah, E. / Zahn, M. / Chen, X. / Kato, R. / Hinchen, D.J. / Konev, M.O. / Katahira, R. / Orr, C. / Wagner, A. / Zou, Y. / Haugen, S.J. / Ramirez, K.J. / Michener, J.K. / Pickford, A.R. / Kamimura, N. / Masai, E. / Houk, K.N. / McGeehan, J.E. / Beckham, G.T.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SnoaL-like domain-containing protein
B: SnoaL-like domain-containing protein
C: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7824
Polymers86,4623
Non-polymers3201
Water11,656647
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.384, 66.002, 107.051
Angle α, β, γ (deg.)90.000, 108.675, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSAA8 - 2418 - 241
221LYSLYSBB8 - 2418 - 241
332TRPTRPAA8 - 2428 - 242
442TRPTRPCC8 - 2428 - 242
553LYSLYSBB7 - 2417 - 241
663LYSLYSCC7 - 2417 - 241

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 28820.516 Da / Num. of mol.: 3 / Mutation: H97Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Strain: ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199
Gene: Saro_2805 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G4I2
#2: Chemical ChemComp-LJU / (1S,2R)-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol


Mass: 320.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 500 MME, 10% PEG 20000, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M Imidazole/MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.661→56.234 Å / Num. obs: 69923 / % possible obs: 94 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Net I/σ(I): 12.8
Reflection shellResolution: 1.661→1.804 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.144 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3497 / CC1/2: 0.653 / Rpim(I) all: 0.467 / % possible all: 55.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XXX

7xxx


Resolution: 1.661→56.234 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.036 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2009 3285 4.698 %
Rwork0.167 66639 -
all0.169 --
obs-69923 79.105 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.674 Å2
Baniso -1Baniso -2Baniso -3
1-0.197 Å20 Å20.14 Å2
2---0.037 Å2-0 Å2
3----0.207 Å2
Refinement stepCycle: LAST / Resolution: 1.661→56.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5709 0 23 647 6379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135901
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165437
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6428009
X-RAY DIFFRACTIONr_angle_other_deg1.4611.58612487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54921.959342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42915943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8361542
X-RAY DIFFRACTIONr_chiral_restr0.090.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
X-RAY DIFFRACTIONr_nbd_refined0.2140.21193
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.25058
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22830
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2628
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1960.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.217
X-RAY DIFFRACTIONr_nbd_other0.2080.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_mcbond_it2.1752.6472816
X-RAY DIFFRACTIONr_mcbond_other2.1752.6462815
X-RAY DIFFRACTIONr_mcangle_it3.363.9483510
X-RAY DIFFRACTIONr_mcangle_other3.363.953511
X-RAY DIFFRACTIONr_scbond_it2.5092.9023085
X-RAY DIFFRACTIONr_scbond_other2.5092.9043086
X-RAY DIFFRACTIONr_scangle_it3.9184.2584499
X-RAY DIFFRACTIONr_scangle_other3.9174.264500
X-RAY DIFFRACTIONr_lrange_it6.26531.6227125
X-RAY DIFFRACTIONr_lrange_other6.03530.8666913
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.057445
X-RAY DIFFRACTIONr_ncsr_local_group_20.0730.057287
X-RAY DIFFRACTIONr_ncsr_local_group_30.070.057405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.067180.05009
12BX-RAY DIFFRACTIONLocal ncs0.067180.05009
23AX-RAY DIFFRACTIONLocal ncs0.073070.05009
24CX-RAY DIFFRACTIONLocal ncs0.073070.05009
35BX-RAY DIFFRACTIONLocal ncs0.070360.05009
36CX-RAY DIFFRACTIONLocal ncs0.070360.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.661-1.7040.23140.299167X-RAY DIFFRACTION2.6279
1.704-1.7510.291370.257918X-RAY DIFFRACTION15.0678
1.751-1.8010.276970.2472090X-RAY DIFFRACTION35.6073
1.801-1.8570.2911960.2473900X-RAY DIFFRACTION68.2212
1.857-1.9180.2582760.2424829X-RAY DIFFRACTION87.7751
1.918-1.9850.2642580.2285237X-RAY DIFFRACTION97.3083
1.985-2.060.2422760.2055138X-RAY DIFFRACTION99.7605
2.06-2.1440.2232300.1854985X-RAY DIFFRACTION100
2.144-2.2390.2222360.1694751X-RAY DIFFRACTION99.9799
2.239-2.3490.1962210.1624588X-RAY DIFFRACTION99.9792
2.349-2.4760.1912120.1534346X-RAY DIFFRACTION99.9781
2.476-2.6260.1922160.154127X-RAY DIFFRACTION100
2.626-2.8070.1931760.1523865X-RAY DIFFRACTION100
2.807-3.0310.1921850.1583608X-RAY DIFFRACTION100
3.031-3.320.1921530.1623347X-RAY DIFFRACTION100
3.32-3.7120.2031390.1563012X-RAY DIFFRACTION99.9049
3.712-4.2850.1511360.142659X-RAY DIFFRACTION100
4.285-5.2460.1681130.1332280X-RAY DIFFRACTION99.9582
5.246-7.4090.209930.1781770X-RAY DIFFRACTION100
7.409-56.2340.24320.2011022X-RAY DIFFRACTION99.5279
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)
10.64580.11240.01340.0427-0.00760.0048-0.01550.10740.0660.02410.0101-0.0058-0.01190.0060.00540.0351-0.0048-0.0150.03190.01880.026731.90591.076724.8415
20.2348-0.16550.00820.185-0.02710.00720.01840.04720.00490.0059-0.0020.0544-0.0042-0.009-0.01650.01910.00910.00740.02940.02550.05447.1499-3.018224.3983
30.2773-0.06310.00940.2587-0.0210.00560.01930.0378-0.0942-0.0273-0.00960.00930.00980.0074-0.00970.02520.0097-0.01360.0189-0.02190.038922.6769-22.199325.0352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA8 - 242
2X-RAY DIFFRACTION2ALLB3 - 242
3X-RAY DIFFRACTION3ALLC7 - 242

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