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- PDB-2xed: Nocardia farcinica maleate cis-trans isomerase C194S mutant with ... -

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Basic information

Entry
Database: PDB / ID: 2xed
TitleNocardia farcinica maleate cis-trans isomerase C194S mutant with a covalently bound succinylcysteine intermediate
ComponentsPUTATIVE MALEATE ISOMERASE
KeywordsISOMERASE / NICOTINIC ACID CATABOLISM / COFACTOR-INDEPENDENT CIS-TRANS ISOMERASE
Function / homology
Function and homology information


maleate isomerase / maleate isomerase activity
Similarity search - Function
Maleate isomerase / Maleate isomerase/Arylmalonate decarboxylase / Arylmalonate decarboxylase / Rossmann fold - #12500 / : / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Maleate isomerase
Similarity search - Component
Biological speciesNOCARDIA FARCINICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFisch, F. / Martinez-Fleites, C. / Baudendistel, N. / Hauer, B. / Turkenburg, J.P. / Hart, S. / Bruce, N.C. / Grogan, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: A Covalent Succinylcysteine-Like Intermediate in the Enzyme-Catalyzed Transformation of Maleate to Fumarate by Maleate Isomerase.
Authors: Fisch, F. / Fleites, C.M. / Delenne, M. / Baudendistel, N. / Hauer, B. / Turkenburg, J.P. / Hart, S. / Bruce, N.C. / Grogan, G.
History
DepositionMay 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: PUTATIVE MALEATE ISOMERASE
B: PUTATIVE MALEATE ISOMERASE
C: PUTATIVE MALEATE ISOMERASE
D: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7808
Polymers115,3084
Non-polymers4724
Water11,440635
1
A: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9452
Polymers28,8271
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9452
Polymers28,8271
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9452
Polymers28,8271
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9452
Polymers28,8271
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.980, 85.670, 239.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PUTATIVE MALEATE ISOMERASE


Mass: 28826.975 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN CYS76 AND SUCCINYL LIKE INTERMEDIATE
Source: (gene. exp.) NOCARDIA FARCINICA (bacteria) / Strain: IFM 10152 / Description: NOCARDIA FARCINICA GENOME PROJECT / Plasmid: PET-YSBLIC3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA2 (DE3) / References: UniProt: Q5YXQ1, maleate isomerase
#2: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 194 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 194 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 194 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 194 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 194 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 194 TO ALA
Nonpolymer detailsSUCCINYL-LIKE COVALENT INTERMEDIATE (SIN): COVALENTLY LINKED TO CYS76
Sequence detailsC194A

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6.5
Details: 20 MM NH4 FORMATE 100 MM MES PH 6.5 20% PEG 3350 50 MM NA MALEATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.95→52.98 Å / Num. obs: 80183 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XEC

2xec


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.723 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 3997 5 %RANDOM
Rwork0.22214 ---
obs0.22402 75994 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.907 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7289 0 32 635 7956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227457
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.98710144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94522.986288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.127151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1151573
X-RAY DIFFRACTIONr_chiral_restr0.0970.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215609
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4651.54929
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84527905
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63432528
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5814.52236
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 303 -
Rwork0.304 5494 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8091-0.21090.55281.74520.01621.55020.00350.2466-0.1636-0.0538-0.05990.193-0.0224-0.01190.05640.01-0.01280.02030.123-0.0760.13483.86061.311135.3164
21.6752-0.3284-0.62142.49850.77062.2221-0.1109-0.09420.08340.19260.0889-0.21990.366-0.0530.0220.1501-0.0248-0.03070.0845-0.02770.0599-17.4595-34.874125.3897
32.20670.65181.12531.32330.92943.14390.0563-0.1835-0.1075-0.155-0.1034-0.0647-0.1477-0.03450.04710.17390.06660.0220.10260.01870.050615.49574.99724.2852
41.7726-0.26560.84241.6058-0.34153.5311-0.0573-0.2685-0.22370.41070.09060.01190.54510.0903-0.03330.28510.05070.02940.08770.00990.067818.5355-5.451663.8209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 248
2X-RAY DIFFRACTION2B1 - 246
3X-RAY DIFFRACTION3C2 - 246
4X-RAY DIFFRACTION4D2 - 246

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