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- PDB-1jof: Neurospora crassa 3-carboxy-cis,cis-mucoante lactonizing enzyme -

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Basic information

Entry
Database: PDB / ID: 1jof
TitleNeurospora crassa 3-carboxy-cis,cis-mucoante lactonizing enzyme
ComponentsCARBOXY-CIS,CIS-MUCONATE CYCLASE
KeywordsISOMERASE / BETA-PROPELLER / HOMOTETRAMER / SEMET-PROTEIN
Function / homology
Function and homology information


carboxy-cis,cis-muconate cyclase / carboxy-cis,cis-muconate cyclase activity / 6-phosphogluconolactonase activity / beta-ketoadipate pathway
Similarity search - Function
: / Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Carboxy-cis,cis-muconate cyclase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKajander, T. / Merckel, M.C. / Thompson, A. / Deacon, A.M. / Mazur, P. / Kozarich, J.W. / Goldman, A.
Citation
Journal: Structure / Year: 2002
Title: The structure of Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme, a beta propeller cycloisomerase.
Authors: Kajander, T. / Merckel, M.C. / Thompson, A. / Deacon, A.M. / Mazur, P. / Kozarich, J.W. / Goldman, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: 3-Carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenomethionines
Authors: Merckel, M.C. / Kajander, T. / Deacon, A.M. / Thompson, A. / Grossmann, J.G. / Kalkkinen, N. / Goldman, A.
History
DepositionJul 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: CARBOXY-CIS,CIS-MUCONATE CYCLASE
B: CARBOXY-CIS,CIS-MUCONATE CYCLASE
C: CARBOXY-CIS,CIS-MUCONATE CYCLASE
D: CARBOXY-CIS,CIS-MUCONATE CYCLASE
E: CARBOXY-CIS,CIS-MUCONATE CYCLASE
F: CARBOXY-CIS,CIS-MUCONATE CYCLASE
G: CARBOXY-CIS,CIS-MUCONATE CYCLASE
H: CARBOXY-CIS,CIS-MUCONATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,34734
Polymers333,7238
Non-polymers2,62326
Water12,845713
1
A: CARBOXY-CIS,CIS-MUCONATE CYCLASE
B: CARBOXY-CIS,CIS-MUCONATE CYCLASE
C: CARBOXY-CIS,CIS-MUCONATE CYCLASE
D: CARBOXY-CIS,CIS-MUCONATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17317
Polymers166,8624
Non-polymers1,31213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: CARBOXY-CIS,CIS-MUCONATE CYCLASE
F: CARBOXY-CIS,CIS-MUCONATE CYCLASE
G: CARBOXY-CIS,CIS-MUCONATE CYCLASE
H: CARBOXY-CIS,CIS-MUCONATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17317
Polymers166,8624
Non-polymers1,31213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.290, 160.600, 237.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe functional biological unit of CMLE is a hometetramer. The asymmetric unit contains two tetramers.

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Components

#1: Protein
CARBOXY-CIS,CIS-MUCONATE CYCLASE / E.C.5.5.1.5 / 3-carboxy-cis / cis-muconate lactonizing enzyme / CMLE


Mass: 41715.414 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli (E. coli)
References: UniProt: P38677, carboxy-cis,cis-muconate cyclase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: PIPES, Ammonium suplhate, beta-mercapto-ethanol, pH 5.7, VAPOR DIFFUSION, SITTING DROP at 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9137, 0.9786, 0.9795, 0.8856
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91371
20.97861
30.97951
40.88561
ReflectionResolution: 2.5→20 Å / Num. all: 122302 / Num. obs: 122302 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 5
Reflection shellResolution: 2.5→2.6 Å / Num. unique all: 0 / Rsym value: 15.6 / % possible all: 75.8
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
SnBphasing
CCP4model building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 6115 5 %random
Rwork0.212 ---
all-122302 --
obs-122302 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22984 0 140 713 23837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.786
X-RAY DIFFRACTIONc_bond_d0.014
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.214 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

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