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- PDB-4p93: Structure of Dienelactone Hydrolase at 1.85 A resolution crystall... -

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Basic information

Entry
Database: PDB / ID: 4p93
TitleStructure of Dienelactone Hydrolase at 1.85 A resolution crystallised in the C2 space group
ComponentsCarboxymethylenebutenolidase
KeywordsHYDROLASE / a/b hydrolase fold
Function / homology
Function and homology information


carboxymethylenebutenolidase / carboxymethylenebutenolidase activity / catabolic process
Similarity search - Function
: / Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxymethylenebutenolidase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPorter, J.L. / Carr, P.D. / Collyer, C.A. / Ollis, D.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing.
Authors: Porter, J.L. / Carr, P.D. / Collyer, C.A. / Ollis, D.L.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: 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: Carboxymethylenebutenolidase
B: Carboxymethylenebutenolidase


Theoretical massNumber of molelcules
Total (without water)50,9912
Polymers50,9912
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-0 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.230, 49.050, 89.610
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 233 / Label seq-ID: 1 - 233

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Carboxymethylenebutenolidase / Dienelactone hydrolase / DLH


Mass: 25495.746 Da / Num. of mol.: 2 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: B13 / Gene: clcD / Production host: Escherichia coli (E. coli) / References: UniProt: P0A115, carboxymethylenebutenolidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→89.36 Å / Num. obs: 35229 / % possible obs: 94 % / Redundancy: 3.2 % / Net I/σ(I): 16.89
Reflection shellResolution: 1.85→1.9 Å / Mean I/σ(I) obs: 5.1 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZI6

1zi6


Resolution: 1.85→89.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.688 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20536 1770 5 %RANDOM
Rwork0.1729 ---
obs0.1746 33459 94.01 %-
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: 21.068 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.31 Å2
2--0.98 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.85→89.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 0 184 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9474969
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13823.905169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84715533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3471520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212881
X-RAY DIFFRACTIONr_gen_planes_other
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 265 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 117 -
Rwork0.201 2299 -
obs--88.76 %

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