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- PDB-3muc: MUCONATE CYCLOISOMERASE VARIANT I54V -

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Basic information

Entry
Database: PDB / ID: 3muc
TitleMUCONATE CYCLOISOMERASE VARIANT I54V
ComponentsPROTEIN (MUCONATE CYCLOISOMERASE)
KeywordsISOMERASE / MUCONATE CYCLOISOMERASE / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


muconate cycloisomerase / chloromuconate cycloisomerase activity / muconate cycloisomerase activity / beta-ketoadipate pathway / 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
: / Muconate cycloisomerase 1
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsSchell, U. / Helin, S. / Kajander, T. / Schlomann, M. / Goldman, A.
Citation
Journal: Proteins / Year: 1999
Title: Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates.
Authors: Schell, U. / Helin, S. / Kajander, T. / Schlomann, M. / Goldman, A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Refined X-Ray Structure of Muconate Lactonizing Enzyme from Pseudomonas Putida Prs2000 at 1.85 A Resolution
Authors: Helin, S. / Kahn, P.C. / Guha, B.L. / Mallows, D.G. / Goldman, A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystal Structure of Chloromuconate Cycloisomerase from Alcaligenes Eutrophus Jmp134 (Pjp4) at 3 A Resolution
Authors: Hoier, H. / Schloemann, M. / Hammer, A. / Glusker, J.P. / Carrell, H.L. / Goldman, A. / Stezowski, J.J. / Heinemann, U.
History
DepositionOct 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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_ref_seq_dif / 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_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MUCONATE CYCLOISOMERASE)
B: PROTEIN (MUCONATE CYCLOISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8394
Polymers79,7292
Non-polymers1102
Water4,594255
1
A: PROTEIN (MUCONATE CYCLOISOMERASE)
B: PROTEIN (MUCONATE CYCLOISOMERASE)
hetero molecules

A: PROTEIN (MUCONATE CYCLOISOMERASE)
B: PROTEIN (MUCONATE CYCLOISOMERASE)
hetero molecules

A: PROTEIN (MUCONATE CYCLOISOMERASE)
B: PROTEIN (MUCONATE CYCLOISOMERASE)
hetero molecules

A: PROTEIN (MUCONATE CYCLOISOMERASE)
B: PROTEIN (MUCONATE CYCLOISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,35616
Polymers318,9178
Non-polymers4408
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area24560 Å2
ΔGint-166 kcal/mol
Surface area90570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.600, 139.600, 84.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.754163, 0.656679, 0.003275), (0.656674, -0.75417, 0.002403), (0.004048, 0.000338, -0.999992)
Vector: 0.0319, -0.0058, -0.0878)

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Components

#1: Protein PROTEIN (MUCONATE CYCLOISOMERASE) / MUCONATE LACTONIZING ENZYME


Mass: 39864.570 Da / Num. of mol.: 2 / Mutation: I54V / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: PRS2000 / References: UniProt: P08310, muconate 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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: double dialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMMES11
22 mM11MnCl2
350 mM11NaCl
40.02 %(w/v)11NaN3
57 mMbeta-mercaptoethanol11
68 mg/mlprotein11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 132958 / % possible obs: 80.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.121
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 30586 / Num. measured all: 132958

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1516 5.1 %RANDOM
Rwork0.176 ---
obs0.176 29720 84.5 %-
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5458 0 2 255 5715
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.451.5
X-RAY DIFFRACTIONx_mcangle_it3.482
X-RAY DIFFRACTIONx_scbond_it5.162
X-RAY DIFFRACTIONx_scangle_it8.242.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 185 4.6 %
Rwork0.211 3840 -
obs--68.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_JPP.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION3PARAMETER.ELEMENTSTOPH19.SOL_WAT
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.211

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