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- PDB-3fa3: Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isoci... -

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Basic information

Entry
Database: PDB / ID: 3fa3
TitleCrystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form
Components2,3-dimethylmalate lyase
KeywordsLYASE / alpha/beta barrel / HELIX SWAPPING
Function / homology
Function and homology information


hydrolase activity / lyase activity / metal ion binding
Similarity search - Function
Phosphoenolpyruvate phosphomutase / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / 2,2-difluoro-3,3-dihydroxybutanedioic acid / Oxaloacetate hydrolase class protein
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNarayanan, B.C. / Herzberg, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member.
Authors: Narayanan, B. / Niu, W. / Joosten, H.J. / Li, Z. / Kuipers, R.K. / Schaap, P.J. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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: 2,3-dimethylmalate lyase
B: 2,3-dimethylmalate lyase
C: 2,3-dimethylmalate lyase
D: 2,3-dimethylmalate lyase
E: 2,3-dimethylmalate lyase
F: 2,3-dimethylmalate lyase
G: 2,3-dimethylmalate lyase
H: 2,3-dimethylmalate lyase
I: 2,3-dimethylmalate lyase
J: 2,3-dimethylmalate lyase
K: 2,3-dimethylmalate lyase
L: 2,3-dimethylmalate lyase
M: 2,3-dimethylmalate lyase
N: 2,3-dimethylmalate lyase
O: 2,3-dimethylmalate lyase
P: 2,3-dimethylmalate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,27251
Polymers512,32816
Non-polymers3,94435
Water12,683704
1
A: 2,3-dimethylmalate lyase
B: 2,3-dimethylmalate lyase
C: 2,3-dimethylmalate lyase
D: 2,3-dimethylmalate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,23014
Polymers128,0824
Non-polymers1,14810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20950 Å2
ΔGint-171 kcal/mol
Surface area37440 Å2
MethodPISA
2
E: 2,3-dimethylmalate lyase
F: 2,3-dimethylmalate lyase
G: 2,3-dimethylmalate lyase
H: 2,3-dimethylmalate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,23014
Polymers128,0824
Non-polymers1,14810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21120 Å2
ΔGint-173 kcal/mol
Surface area37260 Å2
MethodPISA
3
I: 2,3-dimethylmalate lyase
J: 2,3-dimethylmalate lyase
K: 2,3-dimethylmalate lyase
L: 2,3-dimethylmalate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,86011
Polymers128,0824
Non-polymers7787
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20360 Å2
ΔGint-165 kcal/mol
Surface area38270 Å2
MethodPISA
4
M: 2,3-dimethylmalate lyase
N: 2,3-dimethylmalate lyase
O: 2,3-dimethylmalate lyase
P: 2,3-dimethylmalate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,95212
Polymers128,0824
Non-polymers8708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint-168 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.570, 160.570, 161.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
2,3-dimethylmalate lyase


Mass: 32020.477 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: An07g08390 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2L887, EC: 4.1.3.32
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-OAF / 2,2-difluoro-3,3-dihydroxybutanedioic acid


Mass: 186.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H4F2O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 7.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 11, 2007 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 135034 / Num. obs: 135034 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 5.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.9 / Num. unique all: 9535 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 28.895 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6752 5 %RANDOM
Rwork0.19 ---
obs0.193 135026 94.3 %-
all-135034 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35442 0 214 704 36360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02236143
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.96748956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.72854777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10923.2981495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.25155875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.62715334
X-RAY DIFFRACTIONr_chiral_restr0.1370.25646
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227306
X-RAY DIFFRACTIONr_nbd_refined0.2560.219859
X-RAY DIFFRACTIONr_nbtor_refined0.3220.224867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.21785
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.213
X-RAY DIFFRACTIONr_mcbond_it0.6531.524297
X-RAY DIFFRACTIONr_mcangle_it0.872237685
X-RAY DIFFRACTIONr_scbond_it1.631313108
X-RAY DIFFRACTIONr_scangle_it2.3434.511271
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 459 -
Rwork0.298 9058 -
obs-9058 90.01 %
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)
11.42440.0880.14161.1149-0.13360.9551-0.0773-0.0799-0.19940.03220.0728-0.06630.1540.00550.0046-0.06470.02420.0381-0.1857-0.0002-0.2182-11.452-26.4620.77
20.9589-0.05850.0761.0139-0.08491.1047-0.01940.251-0.1411-0.23330.01860.05620.2547-0.13070.00070.0061-0.09360.0116-0.0598-0.0454-0.1878-27.29-27.139-24.704
31.46390.2803-0.10150.9328-0.05630.6934-0.0575-0.02570.15080.06110.07220.0477-0.067-0.1095-0.0147-0.08090.04380.0183-0.16390.0025-0.1957-31.2553.254-3.397
41.2764-0.1804-0.35561.0071-0.04270.8187-0.0570.16310.1961-0.13840.0544-0.0628-0.0136-0.01460.0026-0.0795-0.01610.0584-0.18570.0016-0.1652-7.8312.864-22.064
51.60250.09150.01460.89860.12181.0644-0.0979-0.14450.18250.04720.08560.0809-0.1987-0.02710.0123-0.06770.0222-0.0298-0.1844-0.0028-0.230611.315-66.2780.821
61.1411-0.1937-0.28870.97980.09441.085-0.04850.23150.1405-0.26140.0349-0.0454-0.23290.14430.0136-0.009-0.0959-0.028-0.05560.0484-0.188127.248-65.566-24.701
71.20650.02080.05881.0460.09650.6916-0.0646-0.0818-0.15380.05710.0844-0.05620.06880.1066-0.0198-0.10240.0357-0.0155-0.1504-0.0127-0.206231.239-95.935-3.392
80.8294-0.08980.30921.0518-0.07160.9113-0.03180.1788-0.1605-0.14250.03410.08830.04160.042-0.0023-0.0803-0.0237-0.0601-0.1707-0.0005-0.17857.808-95.614-22.011
91.1273-0.4902-0.02630.8822-0.05481.00560.0028-0.0043-0.2693-0.14460.07920.10280.0319-0.043-0.082-0.02560.12290.03720.02860.15890.0169-33.708-64.21530.781
100.9648-0.26820.10331.471-0.02720.7316-0.106-0.42860.09830.19620.1706-0.0961-0.0830.0196-0.0647-0.00660.17780.06850.21740.0603-0.0435-21.871-43.61650.094
111.7307-0.3625-0.12041.5174-0.09551.37290.1107-0.0063-0.0224-0.1728-0.02730.034-0.101-0.1696-0.08350.02310.17790.07950.02970.1221-0.1351-49.633-32.17327.514
121.2096-0.4141-0.00861.2864-0.04030.9376-0.2133-0.5035-0.22040.18610.26170.2961-0.0062-0.2112-0.04840.04130.22330.16960.40240.27290.0283-57.464-45.53453.154
130.90560.2218-0.05991.5736-0.16760.9038-0.00860.1595-0.03150.02220.08350.26280.0011-0.038-0.07490.1419-0.03930.1596-0.11620.02120.0054-72.408-95.61-23.077
141.15820.21420.04211.2611-0.14550.7991-0.0173-0.1091-0.08060.46540.0714-0.1381-0.04390.0687-0.05410.32350.01220.074-0.1117-0.014-0.0356-48.685-95.561-3.7
151.2832-0.0392-0.47332.19170.10311.2803-0.09090.07240.0712-0.05990.17980.0362-0.19390.0081-0.08890.1566-0.08860.1373-0.10940.0042-0.1386-52.743-65.78-26.263
161.1520.2768-0.26211.8170.00961.0159-0.0542-0.07880.16130.61120.10610.3799-0.1293-0.0822-0.05190.48250.0580.2958-0.0779-0.00870.0023-68.194-65.7-0.637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 302
2X-RAY DIFFRACTION2B2 - 301
3X-RAY DIFFRACTION3C3 - 302
4X-RAY DIFFRACTION4D2 - 302
5X-RAY DIFFRACTION5E2 - 301
6X-RAY DIFFRACTION6F2 - 301
7X-RAY DIFFRACTION7G3 - 302
8X-RAY DIFFRACTION8H3 - 302
9X-RAY DIFFRACTION9I3 - 301
10X-RAY DIFFRACTION10J3 - 302
11X-RAY DIFFRACTION11K2 - 301
12X-RAY DIFFRACTION12L3 - 302
13X-RAY DIFFRACTION13M2 - 301
14X-RAY DIFFRACTION14N3 - 302
15X-RAY DIFFRACTION15O2 - 302
16X-RAY DIFFRACTION16P3 - 302

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