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- PDB-1muc: STRUCTURE OF MUCONATE LACTONIZING ENZYME AT 1.85 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1muc
TitleSTRUCTURE OF MUCONATE LACTONIZING ENZYME AT 1.85 ANGSTROMS RESOLUTION
ComponentsMUCONATE LACTONIZING ENZYME
KeywordsISOMERASE / MUCONATE LACTONIZING ENZYME
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 / Resolution: 1.85 Å
AuthorsHelin, S. / Kahn, P.C. / Guha, B.H.L. / Mallows, D.J. / Goldman, A.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal Structure of Muconate Lactonizing Enzyme at 3 A Resolution
Authors: Goldman, A. / Ollis, D.L. / Steitz, T.A.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Crystal Structure of Muconate Lactonizing Enzyme at 6.5 A Resolution
Authors: Goldman, A. / Ollis, D. / Ngai, K.L. / Steitz, T.A.
History
DepositionSep 20, 1995Processing site: BNL
SupersessionJul 11, 1996ID: 1MLE
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Assembly

Deposited unit
A: MUCONATE LACTONIZING ENZYME
B: MUCONATE LACTONIZING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8204
Polymers80,7102
Non-polymers1102
Water5,531307
1
A: MUCONATE LACTONIZING ENZYME
B: MUCONATE LACTONIZING ENZYME
hetero molecules

A: MUCONATE LACTONIZING ENZYME
B: MUCONATE LACTONIZING ENZYME
hetero molecules

A: MUCONATE LACTONIZING ENZYME
B: MUCONATE LACTONIZING ENZYME
hetero molecules

A: MUCONATE LACTONIZING ENZYME
B: MUCONATE LACTONIZING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,28116
Polymers322,8418
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 area24290 Å2
ΔGint-162 kcal/mol
Surface area90340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.300, 139.300, 84.100
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: (0.7537, 0.6572, 0.0035), (0.6572, -0.7537, 0.0023), (0.0042, 0.0006, -1)
Vector: 0.0634, -0.0139, -0.1482)

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Components

#1: Protein MUCONATE LACTONIZING ENZYME / / CIC / CIS MUCONATE CYCLOISOMERASE


Mass: 40355.172 Da / Num. of mol.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 52 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 1, 1985
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 66609 / % possible obs: 87.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.093
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 8 Å / Num. obs: 59010 / Num. measured all: 191642 / Rmerge(I) obs: 0.193

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.85→8 Å / σ(F): 1
Details: FOR RESIDUE ARG A 20 ELECTRON DENSITY WAS VISIBLE ONLY FOR BACKBONE ATOMS.
RfactorNum. reflection% reflection
Rwork0.168 --
obs0.168 59010 87.2 %
Displacement parametersBiso mean: 21 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 2 307 5760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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