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- PDB-6rqa: Crystal structure of the iminosuccinate reductase of Paracoccus d... -

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Basic information

Entry
Database: PDB / ID: 6rqa
TitleCrystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex with NAD+
Componentsiminosuccinate reductase
KeywordsOXIDOREDUCTASE / iminosuccinate reductase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / glycolate catabolic process / NADH binding / glyoxylate catabolic process
Similarity search - Function
Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tb-Xo4 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TERBIUM(III) ION / Iminosuccinate reductase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 Å
AuthorsZarzycki, J. / Severi, F. / Schada von Borzyskowski, L. / Erb, T.J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB987 Germany
European UnionFET686330 Germany
CitationJournal: Nature / Year: 2019
Title: Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.
Authors: Schada von Borzyskowski, L. / Severi, F. / Kruger, K. / Hermann, L. / Gilardet, A. / Sippel, F. / Pommerenke, B. / Claus, P. / Cortina, N.S. / Glatter, T. / Zauner, S. / Zarzycki, J. / ...Authors: Schada von Borzyskowski, L. / Severi, F. / Kruger, K. / Hermann, L. / Gilardet, A. / Sippel, F. / Pommerenke, B. / Claus, P. / Cortina, N.S. / Glatter, T. / Zauner, S. / Zarzycki, J. / Fuchs, B.M. / Bremer, E. / Maier, U.G. / Amann, R.I. / Erb, T.J.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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
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: iminosuccinate reductase
B: iminosuccinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6537
Polymers72,4522
Non-polymers2,2015
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-48 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.386, 72.407, 164.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein iminosuccinate reductase


Mass: 36226.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_3918 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1B8Z0
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#4: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.2 Å3/Da / Density % sol: 44.19 % / Description: thick plates
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: His-tagged iminosuccinate reductase (10 mg/ml) in buffer containing 25 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM MgCl2, 0.1 mM DTT, 5 mM Tb-Xo4, and 5 mM NAD+ was mixed in a ratio of 1:1 with ...Details: His-tagged iminosuccinate reductase (10 mg/ml) in buffer containing 25 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM MgCl2, 0.1 mM DTT, 5 mM Tb-Xo4, and 5 mM NAD+ was mixed in a ratio of 1:1 with crystallization buffer containing 200 mM Mg(NO3)2 and 20% (w/v) PEG3350 (pH 5.9).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.56→29.4 Å / Num. obs: 20152 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.105 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.56-2.76.50.5271.41872328930.2240.5730.5273.3100
2.7-2.866.80.3692.11871427340.1520.40.3694.7100
2.86-3.066.70.2632.91717425800.110.2860.2636.2100
3.06-3.36.40.1654.51522223970.0710.180.1659.1100
3.3-3.626.70.1086.71507422370.0450.1170.10814.2100
3.62-4.056.50.0818.71314820170.0340.0880.08118.5100
4.05-4.676.30.06310.61145618060.0270.0690.06323.2100
4.67-5.726.40.05811.4987915450.0250.0630.05822.9100
5.72-8.160.05611.8737212300.0240.0610.05622.2100
8.1-29.4015.40.04214.838177130.0190.0460.04228.798

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMO

1omo


Resolution: 2.56→29.4 Å / SU ML: 0.2994 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0579
RfactorNum. reflection% reflection
Rfree0.225 1998 9.95 %
Rwork0.1763 --
obs0.1813 20086 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.24 Å2
Refinement stepCycle: LAST / Resolution: 2.56→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 120 127 5027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365000
X-RAY DIFFRACTIONf_angle_d0.51666783
X-RAY DIFFRACTIONf_chiral_restr0.3198770
X-RAY DIFFRACTIONf_plane_restr0.0033882
X-RAY DIFFRACTIONf_dihedral_angle_d20.98451755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.28561400.2211272X-RAY DIFFRACTION99.86
2.62-2.690.29121410.21291268X-RAY DIFFRACTION99.86
2.69-2.770.34061400.22521266X-RAY DIFFRACTION100
2.77-2.860.3041410.23171269X-RAY DIFFRACTION99.86
2.86-2.970.311390.20731275X-RAY DIFFRACTION99.86
2.97-3.080.2671390.21041256X-RAY DIFFRACTION100
3.08-3.220.26771420.21061279X-RAY DIFFRACTION99.79
3.22-3.390.24691410.19121292X-RAY DIFFRACTION99.93
3.39-3.610.21641430.1731284X-RAY DIFFRACTION100
3.61-3.880.22081420.171295X-RAY DIFFRACTION100
3.88-4.270.1821440.15481294X-RAY DIFFRACTION100
4.27-4.890.19421440.13651305X-RAY DIFFRACTION100
4.89-6.150.22041470.16891329X-RAY DIFFRACTION100
6.15-29.40.16721550.1631404X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 15.8156093028 Å / Origin y: 10.5091906096 Å / Origin z: 54.6297495551 Å
111213212223313233
T0.25930960169 Å2-0.00536292466283 Å20.0397679283008 Å2-0.278247360568 Å2-0.00593287172532 Å2--0.311727288177 Å2
L0.826674936961 °20.0855246190887 °20.728253996311 °2-0.460612595195 °20.154257875543 °2--1.21817678262 °2
S0.0319800982352 Å °0.0194588824755 Å °-0.017826952745 Å °-0.0405351540248 Å °0.0398796306384 Å °-0.00685413978632 Å °0.068097836595 Å °0.0146410320836 Å °-0.0753980019128 Å °
Refinement TLS groupSelection details: all

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