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- PDB-1nu5: Crystal structure of Pseudomonas sp. P51 Chloromuconate lactonizi... -

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Basic information

Entry
Database: PDB / ID: 1nu5
TitleCrystal structure of Pseudomonas sp. P51 Chloromuconate lactonizing enzyme
ComponentsChloromuconate cycloisomerase
KeywordsISOMERASE / enzyme / muconate / dehalogenation
Function / homology
Function and homology information


2,4-dichlorophenoxyacetic acid catabolic process / chloromuconate cycloisomerase / chloromuconate cycloisomerase activity / muconate cycloisomerase activity / amino acid catabolic process / manganese ion binding
Similarity search - Function
Muconate/chloromuconate cycloisomerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...Muconate/chloromuconate cycloisomerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chloromuconate cycloisomerase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKajander, T. / Lehtio, L. / Goldman, A.
CitationJournal: Protein Sci. / Year: 2003
Title: The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.
Authors: Kajander, T. / Lehtio, L. / Schlomann, M. / Goldman, A.
History
DepositionJan 31, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6423
Polymers39,5321
Non-polymers1102
Water5,170287
1
A: Chloromuconate cycloisomerase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)317,13524
Polymers316,2568
Non-polymers87916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
Buried area25170 Å2
ΔGint-204 kcal/mol
Surface area94880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.355, 135.355, 105.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is an octamer generated from the monomer in the asymmetric unit by the four fold axis 0,0,z and by the two fold axis 0,y,0

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Components

#1: Protein Chloromuconate cycloisomerase / / Cl-MLE / Muconate cycloisomerase II / Chloromuconate lactonizing enzyme


Mass: 39531.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: P51 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P27099, chloromuconate cycloisomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.85 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, Mangane chloride, hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMHEPES1reservoirpH7.5
2100 mM1reservoirMnCl2
312 %(w/v)PEG4001reservoir
410 mg/mlprotein1drop
520 mMTris1droppH7.2
62 mM1dropMnCl2
71 mMcis,cis-muconate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.99015 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99015 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 35845 / Num. obs: 35772 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.17 / % possible all: 100
Reflection
*PLUS
Num. measured all: 1063968 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 15.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3235754.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1784 5 %RANDOM
Rwork0.2 ---
all0.2 35772 --
obs0.2 35621 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.3482 Å2 / ksol: 0.375874 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å20 Å20 Å2
2---4.35 Å20 Å2
3---8.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 2 287 3016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it3.151.5
X-RAY DIFFRACTIONc_mcangle_it5.022
X-RAY DIFFRACTIONc_scbond_it6.032
X-RAY DIFFRACTIONc_scangle_it8.682.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 279 4.8 %
Rwork0.228 5551 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.256
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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