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- PDB-2pgw: Crystal structure of a putative muconate cycloisomerase from Sino... -

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Basic information

Entry
Database: PDB / ID: 2pgw
TitleCrystal structure of a putative muconate cycloisomerase from Sinorhizobium meliloti 1021
ComponentsMuconate cycloisomeraseMuconate lactonizing enzyme
KeywordsISOMERASE / Enolase superfamily / Muconate cycloisomerase / Octamer / Small molecule metabolism / PSI-II / NYSGXRC / 9387a / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


muconate cycloisomerase / muconate cycloisomerase activity / amino acid catabolic process
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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 ...Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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
Mandelate racemase/muconate lactonizing enzyme family protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsKumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative muconate cycloisomerase from Sinorhizobium meliloti 1021
Authors: Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Muconate cycloisomerase
B: Muconate cycloisomerase
C: Muconate cycloisomerase
D: Muconate cycloisomerase
E: Muconate cycloisomerase
F: Muconate cycloisomerase
G: Muconate cycloisomerase
H: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,41014
Polymers341,8578
Non-polymers5536
Water30,2471679
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36100 Å2
ΔGint-156 kcal/mol
Surface area86300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.315, 178.139, 115.176
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Muconate cycloisomerase / Muconate lactonizing enzyme


Mass: 42732.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0797, SMa1461 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92YR6, muconate cycloisomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1679 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2M LiSO4, 5% Glycerol, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 234402 / Num. obs: 234402 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 10.1 Å2 / Rsym value: 0.11 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3 / Num. unique all: 20668 / Rsym value: 0.244 / % possible all: 86.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→48.89 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 52552.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 11367 5 %RANDOM
Rwork0.196 ---
obs0.196 228685 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.632 Å2 / ksol: 0.411666 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.88 Å2
2--1.42 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22938 0 36 1679 24653
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.722
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 1693 5 %
Rwork0.237 32333 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5gol.pargol.top

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