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- PDB-6z3b: Low resolution structure of RgNanOx -

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Basic information

Entry
Database: PDB / ID: 6z3b
TitleLow resolution structure of RgNanOx
Components(Gfo/Idh/MocA family oxidoreductase) x 2
KeywordsCARBOHYDRATE / enzyme / sialic acid / epimerase / oxidase / reductase
Function / homologyGfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Gfo/Idh/MocA family oxidoreductase
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsNaismith, J.H. / Lee, M.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria.
Authors: Bell, A. / Severi, E. / Lee, M. / Monaco, S. / Latousakis, D. / Angulo, J. / Thomas, G.H. / Naismith, J.H. / Juge, N.
History
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Jan 24, 2024Group: 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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gfo/Idh/MocA family oxidoreductase
B: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2036
Polymers83,4912
Non-polymers1,7114
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-47 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.100, 150.100, 193.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 1 - 368

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA3 - 370
2BB1 - 368

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Components

#1: Protein Gfo/Idh/MocA family oxidoreductase


Mass: 41946.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria)
Gene: CDL25_11485, CDL27_13940, DW270_01520, DW812_00100, DWY88_14550, DWZ50_08505
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N5NNS3
#2: Protein Gfo/Idh/MocA family oxidoreductase


Mass: 41545.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria)
Gene: CDL25_11485, CDL27_13940, DW270_01520, DW812_00100, DWY88_14550, DWZ50_08505
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N5NNS3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3000, sodium citrate

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→119 Å / Num. obs: 34401 / % possible obs: 98.6 % / Redundancy: 7.5 % / CC1/2: 1 / Net I/σ(I): 7.5
Reflection shellResolution: 2.58→2.7 Å / Num. unique obs: 1871 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UI9

5ui9


Resolution: 2.58→118.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 25.866 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24971 1732 5 %RANDOM
Rwork0.21247 ---
obs0.21428 33071 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2---0.21 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.58→118.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 114 70 5976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136064
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175429
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6418198
X-RAY DIFFRACTIONr_angle_other_deg1.2221.58112639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74123.241324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.692151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9821530
X-RAY DIFFRACTIONr_chiral_restr0.0660.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
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_it1.5053.4632950
X-RAY DIFFRACTIONr_mcbond_other1.5053.4632948
X-RAY DIFFRACTIONr_mcangle_it2.5395.1873682
X-RAY DIFFRACTIONr_mcangle_other2.5395.1873682
X-RAY DIFFRACTIONr_scbond_it1.593.6933112
X-RAY DIFFRACTIONr_scbond_other1.5893.693109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6585.4754514
X-RAY DIFFRACTIONr_long_range_B_refined4.86240.166514
X-RAY DIFFRACTIONr_long_range_B_other4.85340.1376506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11887 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 121 -
Rwork0.376 2412 -
obs--99.49 %
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)
11.2472-0.4093-0.27141.20580.23220.323-0.02650.1052-0.16370.1801-0.02970.37310.0210.08990.05620.0297-0.0050.01860.0603-0.02761.00510.538-16.41632.033
271.9535-20.1677-4.482210.0236-12.378942.8531-6.35131.59092.5881-0.75560.3751-2.69088.5743-2.36695.97622.7766-0.87310.45460.4153-0.07021.300932.011-19.02550.932
31.1921-0.1912-0.00810.8490.30390.77910.03880.00650.174-0.1023-0.0713-0.03160.0448-0.02710.03250.0638-0.0109-0.03410.10770.03260.844431.619-10.34925.485
42.4252-0.95340.08652.06220.02230.1931-0.00490.02650.09040.1217-0.10620.12330.0464-0.10770.11110.0545-0.0201-0.00340.09220.01790.781617.148-12.48329.532
51.25870.337-0.21441.0478-0.26830.4213-0.0287-0.064-0.1016-0.1741-0.0158-0.31280.0449-0.07510.04450.05650.01730.03510.0356-0.0080.964464.498-16.53425.856
62.38234.4447-5.716719.4053-2.182720.2036-0.4406-0.1333-0.6098-1.2973-1.3383-0.83170.7867-0.55181.77890.24440.16780.10420.5426-0.30630.719946.513-20.0728.847
71.768-0.1749-0.05680.32130.05840.03590.0431-0.04220.30140.0756-0.01240.03480.0510.0108-0.03070.08170.0168-0.0350.05-0.04170.932744.784-8.36233.182
82.13450.5047-0.09061.74860.06690.16410.0148-0.02410.1612-0.1666-0.1204-0.10390.07870.0670.10560.08030.0606-0.00360.0593-0.02820.853258.798-12.27727.609
928.47974.51535.051917.606-5.773219.17530.1037-0.5263-0.15230.4984-0.4763-0.18950.03680.05140.37250.26440.0331-0.02120.1014-0.0220.69550.352-33.73734.293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 202
2X-RAY DIFFRACTION2A203 - 208
3X-RAY DIFFRACTION3A209 - 271
4X-RAY DIFFRACTION4A272 - 372
5X-RAY DIFFRACTION5B1 - 202
6X-RAY DIFFRACTION6B203 - 211
7X-RAY DIFFRACTION7B212 - 279
8X-RAY DIFFRACTION8B280 - 362
9X-RAY DIFFRACTION9B363 - 371

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