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- PDB-4xxv: Crystal structure of 3-isopropylmalate dehydrogenase from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 4xxv
TitleCrystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / 3-isopropylmalate dehydrogenase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
Isopropylmalate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4795
Polymers78,6322
Non-polymers8483
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-36 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.350, 60.900, 105.050
Angle α, β, γ (deg.)90.000, 117.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21B-580-

HOH

Detailsbiological unit is a dimer

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Components

#1: Protein 3-isopropylmalate dehydrogenase / 3-IPM-DH / Beta-IPM dehydrogenase / IMDH


Mass: 39315.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: leuB, BTH_II0674 / Plasmid: ButhA.00092.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2T7H6, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytics MCSG1 B7: 25.5% PEG 4000, 15% glycerol, 170mM Ammonium acetate; ButhA.00092.a.B1.PS0xxxx at 12.64 mg/ml; the drop was overlayed with 5ul 5mM NAD in reservoir and soaked over ...Details: Microlytics MCSG1 B7: 25.5% PEG 4000, 15% glycerol, 170mM Ammonium acetate; ButhA.00092.a.B1.PS0xxxx at 12.64 mg/ml; the drop was overlayed with 5ul 5mM NAD in reservoir and soaked over night; cryo: direct; tray 257491b7, puck tiz0-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 15, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 86107 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 13.32 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 0.981 / Net I/σ(I): 30.23 / Num. measured all: 614892
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.743.40.910.2864.1818874652955900.33685.6
1.74-1.790.9560.2595.4726836640057760.2990.2
1.79-1.840.970.2226.2727080617657130.24792.5
1.84-1.90.9760.27.0227428605557110.22394.3
1.9-1.960.9840.13410.8427712581956240.14996.6
1.96-2.030.990.12111.8827929564955560.13598.4
2.03-2.110.9930.09815.3228363546054340.10999.5
2.11-2.190.9960.08420.2233362524952290.09199.6
2.19-2.290.9970.07126.9935622505450410.07799.7
2.29-2.40.9980.06428.8236167482347810.06999.1
2.4-2.530.9990.05434.3537295461346040.05899.8
2.53-2.690.9990.0538.5638245432343140.05499.8
2.69-2.870.9990.04547.4942984411941120.04799.8
2.87-3.110.0453.1142378379137860.04299.9
3.1-3.410.03263.3839702354235340.03499.8
3.4-3.810.02973.8835276318631750.03199.7
3.8-4.3910.02586.2431345283428170.02699.4
4.39-5.3810.02389.8326547238723810.02499.7
5.38-7.610.02876.2920808188318750.02999.6
7.610.02197.5210939107510540.02298

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, 4iwh

4iwh


Resolution: 1.7→43.612 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1738 2000 2.32 %Random selection
Rwork0.149 84097 --
obs0.1495 86097 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.38 Å2 / Biso mean: 15.7571 Å2 / Biso min: 4.49 Å2
Refinement stepCycle: final / Resolution: 1.7→43.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 62 975 6393
Biso mean--13.76 28.13 -
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115615
X-RAY DIFFRACTIONf_angle_d1.3257642
X-RAY DIFFRACTIONf_chiral_restr0.067858
X-RAY DIFFRACTIONf_plane_restr0.0061009
X-RAY DIFFRACTIONf_dihedral_angle_d13.2822099
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.24281250.1915268539386
1.7425-1.78960.24081320.17565556568890
1.7896-1.84230.1881350.17225685582092
1.8423-1.90180.23541390.17455837597694
1.9018-1.96970.1781420.16735970611297
1.9697-2.04860.17231450.15146081622699
2.0486-2.14180.16441460.148861506296100
2.1418-2.25470.18511480.149561966344100
2.2547-2.3960.17171460.15236140628699
2.396-2.5810.18451460.145761806326100
2.581-2.84070.19671480.151761946342100
2.8407-3.25160.16411480.151262366384100
3.2516-4.09620.16451480.134362396387100
4.0962-43.62610.1321520.131163656517100
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)
10.98510.06440.33622.00350.08441.30550.02720.03250.0786-0.0639-0.0674-0.177-0.14620.18310.00380.0586-0.02810.00690.10410.02280.087510.1915.948437.0658
20.70040.06420.10770.9649-0.10360.5350.03280.0612-0.00490.0347-0.0431-0.0908-0.02740.05020.00940.0588-0.00150.00020.06440.00930.0559-10.95724.718719.5129
30.6575-0.42320.31262.02-0.41070.99950.11630.0792-0.1127-0.2087-0.0910.08510.17140.1617-0.01360.08310.0266-0.01220.0821-0.01050.09395.8591-9.105230.2582
40.67970.07960.27731.9826-0.11120.93250.02060.03640.0481-0.0592-0.02510.27280.0034-0.2389-0.02660.04320.0118-0.00940.1152-0.00490.0883-43.24471.42287.479
52.54410.7093-0.13311.5885-0.4341.292-0.06320.1360.1699-0.04140.01130.0634-0.1406-0.08510.05130.0710.0296-0.01080.08350.0030.075-35.331410.133810.1177
60.9923-0.45090.05372.0318-0.01980.64040.0325-0.1071-0.17550.0406-0.01920.06360.0784-0.0762-0.00290.0871-0.0108-0.00480.07760.00140.0665-30.7844-9.613226.0431
70.9310.2549-0.20180.8901-0.20210.62670.0592-0.11550.07640.087-0.05080.0197-0.1199-0.0116-0.00580.0889-0.0010.00420.0818-0.01920.0556-25.92510.157932.1106
80.37110.42970.51870.85920.13661.21190.0423-0.0345-0.04180.0346-0.0037-0.02540.0515-0.0381-0.0460.05530.00640.00990.0665-0.0010.0659-31.1269-2.256621.4644
91.4866-0.8687-0.53161.52540.7980.4866-0.0888-0.2073-0.09060.52470.01290.33050.3144-0.23140.02520.1722-0.05620.04810.16990.00620.1149-45.4482-10.303921.3832
102.1399-1.049-0.18061.9051-0.42341.36690.0838-0.0148-0.41540.1524-0.0477-0.04220.3228-0.13190.01470.1469-0.0364-0.01790.0751-0.00330.1369-36.3354-19.846412.0714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 92 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 256 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 355 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 50 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 92 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 93 through 122 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 123 through 230 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 293 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 327 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 328 through 355 )B0

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