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- PDB-3v4d: Crystal structure of RutC protein a member of the YjgF family fro... -

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Basic information

Entry
Database: PDB / ID: 3v4d
TitleCrystal structure of RutC protein a member of the YjgF family from E.coli
ComponentsAminoacrylate peracid reductase RutC
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


uracil catabolic process / nitrogen utilization / Oxidoreductases / oxidoreductase activity
Similarity search - Function
3-aminoacrylate deaminase RutC / RidA, conserved site / Uncharacterized protein family UPF0076 signature. / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative aminoacrylate peracid reductase RutC
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsKnapik, A.A. / Petkowski, J.J. / Otwinowski, Z. / Cymborowski, M.T. / Cooper, D.R. / Chruszcz, M. / Porebski, P.J. / Niedzialkowska, E. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Escherichia coli RutC, a member of the YjgF family and putative aminoacrylate peracid reductase of the rut operon.
Authors: Knapik, A.A. / Petkowski, J.J. / Otwinowski, Z. / Cymborowski, M.T. / Cooper, D.R. / Chruszcz, M. / Krajewska, W.M. / Minor, W.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references / Structure summary
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Dec 12, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoacrylate peracid reductase RutC
C: Aminoacrylate peracid reductase RutC
F: Aminoacrylate peracid reductase RutC
B: Aminoacrylate peracid reductase RutC
D: Aminoacrylate peracid reductase RutC
E: Aminoacrylate peracid reductase RutC


Theoretical massNumber of molelcules
Total (without water)87,6996
Polymers87,6996
Non-polymers00
Water6,161342
1
A: Aminoacrylate peracid reductase RutC
C: Aminoacrylate peracid reductase RutC
F: Aminoacrylate peracid reductase RutC


Theoretical massNumber of molelcules
Total (without water)43,8493
Polymers43,8493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-38 kcal/mol
Surface area15160 Å2
MethodPISA
2
B: Aminoacrylate peracid reductase RutC
D: Aminoacrylate peracid reductase RutC
E: Aminoacrylate peracid reductase RutC


Theoretical massNumber of molelcules
Total (without water)43,8493
Polymers43,8493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-39 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.255, 179.181, 45.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Aminoacrylate peracid reductase RutC


Mass: 14616.424 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: XL-1 Blue / Gene: c1147, rutC / Plasmid: pET15b modified for TEV cleavage / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3RIL / References: UniProt: P0AFQ6, Oxidoreductases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M MMT, 30% PEG 1500, +xylitol, K/Na tartrate, 2,6-pyridinecarboxylic acid, 2,4-pyridinecarboxylic acid, 2,5-pyridinecarboxylic acid, 4-pyridazine carboxylic acid, 3-sulfobenzoic acid, pH ...Details: 0.1 M MMT, 30% PEG 1500, +xylitol, K/Na tartrate, 2,6-pyridinecarboxylic acid, 2,4-pyridinecarboxylic acid, 2,5-pyridinecarboxylic acid, 4-pyridazine carboxylic acid, 3-sulfobenzoic acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2010
RadiationMonochromator: C (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 55593 / Num. obs: 55593 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 34.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 9 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3 / Num. unique all: 2712 / Rsym value: 0.633 / % possible all: 100

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
SOLVEphasing
RESOLVEmodel building
CCP4model building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.94 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.176 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21658 2816 5.1 %RANDOM
Rwork0.19337 ---
all0.1946 52607 --
obs0.1946 52607 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.366 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---3.17 Å20 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 0 342 5984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.025805
X-RAY DIFFRACTIONr_bond_other_d0.0060.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9537937
X-RAY DIFFRACTIONr_angle_other_deg2.39539116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92324.33224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05615792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9831519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216519
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021164
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 191 -
Rwork0.26 3515 -
obs--99.28 %
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)
11.1620.6215-0.45098.4393-1.8142.0355-0.02380.12620.1637-1.18420.24771.82930.2498-0.1609-0.22390.1698-0.0266-0.2540.17010.02270.421411.02622.0111.132
21.6983-1.27150.11465.57190.08330.97820.0904-0.066-0.3902-0.0659-0.14710.75540.14810.02010.05680.0936-0.00940.00480.1299-0.00680.1442-28.18714.82117.339
30.970.5099-0.27075.9669-1.6771.93710.0186-0.03040.05550.2097-0.3443-0.7128-0.16280.18560.32570.0407-0.0277-0.03770.17220.04420.114130.34829.8318.889
41.6011-1.52480.06826.1668-0.37011.3548-0.1134-0.15090.37050.429-0.0495-1.3519-0.06720.13690.16290.0338-0.0076-0.09730.20740.0230.303-11.63129.26322.138
51.6244-1.0608-0.10264.4044-0.05471.1160.035-0.00090.0864-0.2695-0.13090.4288-0.0763-0.05480.09590.07030.0126-0.03330.1618-0.0230.085-31.31636.88813.79
61.27240.5498-0.23798.8063-1.74811.75340.02010.0038-0.2991-1.0089-0.3155-0.90540.38440.11870.29540.21750.06030.11260.13840.02210.1528.0027.6975.584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 127
2X-RAY DIFFRACTION2B2 - 126
3X-RAY DIFFRACTION3C2 - 127
4X-RAY DIFFRACTION4D2 - 127
5X-RAY DIFFRACTION5E2 - 127
6X-RAY DIFFRACTION6F2 - 127

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