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- PDB-3v48: Crystal Structure of the putative alpha/beta hydrolase RutD from ... -

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Basic information

Entry
Database: PDB / ID: 3v48
TitleCrystal Structure of the putative alpha/beta hydrolase RutD from E.coli
ComponentsPutative aminoacrylate hydrolase RutD
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


uracil catabolic process / nitrogen utilization / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
Similarity search - Function
Pyrimidine utilisation protein RutD / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Putative aminoacrylate hydrolase RutD
Similarity search - Component
Biological speciesEscherichia coli SE11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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: Proteins / Year: 2012
Title: A multi-faceted analysis of RutD reveals a novel family of alpha / beta hydrolases.
Authors: Knapik, A.A. / Petkowski, J.J. / Otwinowski, Z. / Cymborowski, M.T. / Cooper, D.R. / Majorek, K.A. / 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 1.2Jun 6, 2012Group: Database references
Revision 1.3Jun 20, 2012Group: Database references
Revision 1.4Aug 28, 2013Group: Database references
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Apr 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative aminoacrylate hydrolase RutD
B: Putative aminoacrylate hydrolase RutD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3509
Polymers58,8072
Non-polymers5437
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-26 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.597, 79.597, 161.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative aminoacrylate hydrolase RutD / Aminohydrolase


Mass: 29403.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli SE11 (bacteria) / Strain: XL-1 Blue / Gene: ECSE_1071, rutD / Plasmid: pET15b, modified for TEV cleavage / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3RIL
References: UniProt: B6I985, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15 M Malic acid 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: 2.1→50 Å / Num. all: 31045 / Num. obs: 31045 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.352 / Rsym value: 0.352 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1451 / % possible all: 95

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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: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22565 1471 5 %RANDOM
Rwork0.16915 ---
all0.17188 28021 --
obs0.17188 28021 94.57 %-
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: 31.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 33 313 4390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194187
X-RAY DIFFRACTIONr_bond_other_d00.022724
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9715709
X-RAY DIFFRACTIONr_angle_other_deg4.29136652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05523.88183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43915597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2011525
X-RAY DIFFRACTIONr_chiral_restr0.0770.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214721
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02828
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 68 -
Rwork0.19 1686 -
obs--78.34 %
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)
113.42942.2698-2.01794.0091-0.77011.2260.1693-0.8162-0.13240.6266-0.1096-0.2656-0.25070.1654-0.05970.20350.0644-0.01480.277-0.05040.056128.98316.42173.099
22.0215-0.3068-0.60261.23320.02582.0641-0.0502-0.22930.0030.0730.0489-0.02880.07270.2110.00140.03660.0306-0.00780.12890.00320.024833.34812.61361.337
31.4491-0.24710.23650.1766-0.29151.33950.0676-0.11310.23330.01370.027-0.0701-0.19530.2575-0.09460.127-0.04950.03280.1899-0.04340.112636.03425.74544.698
41.4018-0.3145-0.36971.0238-0.16261.6226-0.05890.0764-0.0778-0.03650.08730.10740.06590.0233-0.02840.0495-0.0050.01070.07630.01120.043627.14810.93751.037
50.7426-1.54824.469457.8914-12.958327.30410.1334-0.0403-0.00940.0736-0.06350.57980.9081-0.1514-0.06990.2567-0.06870.0180.2010.05090.044216.4230.53466.316
622.42996.47263.38914.05082.56142.9507-0.27332.27310.2667-0.42610.4229-0.0245-0.59180.2682-0.14950.2138-0.01140.00170.36740.06040.044519.64627.3234.168
72.1026-0.16770.57111.402-0.26553.16690.05750.11230.1226-0.13650.0175-0.0494-0.5330.0044-0.07510.1768-0.00580.02410.06120.02170.034724.15933.04114.692
81.12980.4394-0.230.441-0.13353.02820.03150.0259-0.035-0.10930.0352-0.0814-0.21740.4311-0.06680.0942-0.03720.00570.1427-0.02390.076334.98722.51429.996
97.1798-1.9345-2.45751.90961.07252.70780.1454-0.27980.7229-0.07610.1588-0.1778-0.89140.531-0.30420.4168-0.18990.06560.125-0.02040.111530.27540.43723.396
101.0913-0.1171-0.01841.5746-0.40762.33550.0783-0.03930.0109-0.06590.06820.1462-0.2444-0.4257-0.14650.11790.0570.01210.13070.02530.082514.33529.45526.756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 14
2X-RAY DIFFRACTION2A15 - 116
3X-RAY DIFFRACTION3A117 - 172
4X-RAY DIFFRACTION4A173 - 258
5X-RAY DIFFRACTION5A259 - 266
6X-RAY DIFFRACTION6B0 - 14
7X-RAY DIFFRACTION7B15 - 116
8X-RAY DIFFRACTION8B117 - 172
9X-RAY DIFFRACTION9B173 - 198
10X-RAY DIFFRACTION10B199 - 262

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