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- PDB-2xec: Nocardia farcinica maleate cis-trans isomerase bound to TRIS -

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Basic information

Entry
Database: PDB / ID: 2xec
TitleNocardia farcinica maleate cis-trans isomerase bound to TRIS
ComponentsPUTATIVE MALEATE ISOMERASE
KeywordsISOMERASE
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
Biological speciesNOCARDIA FARCINICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.1Oct 3, 2012Group: Derived calculations / Version format compliance
Revision 1.2Dec 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_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_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)115,7618
Polymers115,4364
Non-polymers3244
Water2,144119
1
A: PUTATIVE MALEATE ISOMERASE
D: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0025
Polymers57,7182
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-5.5 kcal/mol
Surface area18640 Å2
MethodPISA
2
B: PUTATIVE MALEATE ISOMERASE
C: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7583
Polymers57,7182
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-14.2 kcal/mol
Surface area18590 Å2
MethodPISA
3
A: PUTATIVE MALEATE ISOMERASE
D: PUTATIVE MALEATE ISOMERASE
hetero molecules

B: PUTATIVE MALEATE ISOMERASE
C: PUTATIVE MALEATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7618
Polymers115,4364
Non-polymers3244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465x-1/2,-y+3/2,-z1
Buried area3530 Å2
ΔGint-19.7 kcal/mol
Surface area36300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.160, 84.510, 238.130
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: 28859.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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): ROSETTA2 (DE3) / References: UniProt: Q5YXQ1, maleate isomerase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL N-TERMINAL HIS-TAG

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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5
Details: 300 MM CA ACETATE 100 MM TRIS PH 7.5 5 MM NA MALEATE 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→50.16 Å / Num. obs: 52302 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DG9

3dg9


Resolution: 2.2→48.67 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 23.311 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.28841 2661 5.1 %RANDOM
Rwork0.23859 ---
obs0.24112 49570 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--0.44 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 18 119 7377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.98610027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43522.958284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.141151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6841572
X-RAY DIFFRACTIONr_chiral_restr0.1140.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215508
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_it0.6831.54885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1727838
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17932481
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2124.52189
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 196 -
Rwork0.343 3616 -
obs--99.95 %
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)
12.1083-1.22270.86833.0282-0.27163.01450.21330.14760.0096-0.2098-0.1717-0.02370.50340.235-0.04150.26180.0708-0.01230.224-0.01510.19637.401548.826-14.7298
20.5781-0.01180.13793.9039-1.39632.18120.0736-0.0598-0.0944-0.2428-0.03220.20110.6022-0.06-0.04140.3697-0.0549-0.03270.251-0.00930.268814.448433.38313.5661
31.10321.6628-2.35455.2956-3.51489.88650.0717-0.0972-0.0205-0.0930.13390.04680.48430.2256-0.20560.1065-0.0524-0.06530.35910.00530.304519.540844.609744.2117
43.1178-0.02434.08364.10420.716713.46710.04070.3333-0.57850.51860.4044-0.2492-0.29651.3531-0.4450.1228-0.03930.04030.5322-0.14630.431119.559745.2726-45.5562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 248
2X-RAY DIFFRACTION2B1 - 245
3X-RAY DIFFRACTION3C1 - 245
4X-RAY DIFFRACTION4D1 - 246

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