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- PDB-3fa4: Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isoci... -

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Basic information

Entry
Database: PDB / ID: 3fa4
TitleCrystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, triclinic crystal form
Components2,3-dimethylmalate lyase
KeywordsLYASE / alpha/beta barrel / HELIX SWAPPING
Function / homology
Function and homology information


oxaloacetase activity / oxaloacetate metabolic process / isomerase activity / hydrolase 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
Oxaloacetate hydrolase class protein
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,53724
Polymers384,24612
Non-polymers29212
Water20,9331162
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)128,1798
Polymers128,0824
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18980 Å2
ΔGint-157 kcal/mol
Surface area38580 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)128,1798
Polymers128,0824
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-157 kcal/mol
Surface area38830 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)128,1798
Polymers128,0824
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18300 Å2
ΔGint-154 kcal/mol
Surface area38280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.090, 115.470, 115.750
Angle α, β, γ (deg.)119.66, 90.71, 96.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
2,3-dimethylmalate lyase


Mass: 32020.477 Da / Num. of mol.: 12
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG 6000, 0.1M MES, pH 6.5, 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: Feb 27, 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: 2.18→46.83 Å / Num. all: 170912 / Num. obs: 170912 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 5.2
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 2 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 1.7 / Num. unique all: 8280 / % possible all: 69.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FA3

3fa3


Resolution: 2.18→46.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.722 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 8603 5 %RANDOM
Rwork0.2 ---
obs0.204 170843 93.2 %-
all-170912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.18 Å20.08 Å2
2---0.18 Å2-0.11 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.18→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25258 0 12 1162 26432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02225620
X-RAY DIFFRACTIONr_angle_refined_deg2.0881.96334691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.86753384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98523.3021063
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.356154202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.91115241
X-RAY DIFFRACTIONr_chiral_restr0.1460.24038
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219306
X-RAY DIFFRACTIONr_nbd_refined0.2340.212152
X-RAY DIFFRACTIONr_nbtor_refined0.3040.217298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.21289
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.233
X-RAY DIFFRACTIONr_mcbond_it0.851.517509
X-RAY DIFFRACTIONr_mcangle_it1.278226864
X-RAY DIFFRACTIONr_scbond_it2.31139237
X-RAY DIFFRACTIONr_scangle_it3.3524.57827
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 401 -
Rwork0.318 7879 -
obs-7879 61.57 %
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)
11.07850.0383-0.19391.4488-0.15190.53040.0033-0.1067-0.01510.0852-0.0085-0.04130.0631-0.01370.0052-0.0859-0.00980.0199-0.07930.0488-0.1428-3.6389-60.509121.6696
20.82580.0992-0.27171.76390.11291.0737-0.0373-0.01920.0389-0.009-0.0240.0265-0.0257-0.03670.0614-0.19040.0296-0.0182-0.09320.0079-0.1107-5.0968-29.408915.5094
31.11110.0734-0.02560.56580.381.83680.0064-0.0901-0.00010.09510.0265-0.14030.04760.1232-0.0329-0.15370.0227-0.0379-0.07620.0384-0.054429.3678-45.572913.288
41.55630.03250.21980.76470.25111.1769-0.01720.05010.018-0.08430.0103-0.0602-0.01720.03450.0069-0.16590.02450.0043-0.10350.0479-0.159810.3913-48.7466-11.6414
51.71830.4336-0.27071.3773-0.02630.63930.03720.00490.0856-0.06-0.02730.1155-0.101-0.0096-0.0099-0.1050.027-0.0125-0.10650.0644-0.105126.788833.065235.9993
61.05770.0864-0.00222.7365-0.25390.77110.0048-0.01310.0430.019-0.0670.3294-0.0054-0.09120.0622-0.20620.00260.01-0.0662-0.0057-0.0687.55259.807345.3665
70.8776-0.3224-0.0531.28050.15591.5612-0.0029-0.0077-0.0358-0.01630.0439-0.0987-0.07210.0084-0.0411-0.21220.01540.0048-0.10910.0105-0.114842.1478-0.182732.803
81.15690.10860.2210.27520.39991.43670.0186-0.05470.0530.0434-0.05180.0199-0.08-0.06070.0333-0.06860.031-0.053-0.08330.0532-0.084740.00479.947363.014
90.9281-0.0887-0.21.1369-0.16921.5750.06740.0444-0.0979-0.08560.0301-0.13740.08330.1669-0.09750.1040.0332-0.02620.01620.02430.0439-5.5919-65.062373.4971
100.852-0.4728-0.05431.33570.35771.43110.05590.010.01180.0161-0.0173-0.01090.07790.0125-0.03860.0576-0.03360.0235-0.00040.0528-0.0259-19.9186-46.106595.1658
110.7257-0.0622-0.08131.64630.07930.35120.0667-0.0486-0.06350.01570.0115-0.11360.0630.0091-0.07820.0277-0.01960.05650.02090.0242-0.035-4.3231-29.34164.1133
121.43690.7598-0.13351.1643-0.08650.8477-0.00350.05810.027-0.0313-0.02130.14330.004-0.10840.02490.02870.00690.01530.0276-0.00540.0206-33.2994-42.137161.0899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 292
2X-RAY DIFFRACTION2B2 - 292
3X-RAY DIFFRACTION3C4 - 292
4X-RAY DIFFRACTION4D2 - 293
5X-RAY DIFFRACTION5E2 - 294
6X-RAY DIFFRACTION6F3 - 292
7X-RAY DIFFRACTION7G2 - 292
8X-RAY DIFFRACTION8H3 - 292
9X-RAY DIFFRACTION9I4 - 292
10X-RAY DIFFRACTION10J3 - 292
11X-RAY DIFFRACTION11K5 - 293
12X-RAY DIFFRACTION12L5 - 292

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