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- PDB-4iwh: Crystal structure of a 3-isopropylmalate dehydrogenase from Burkh... -

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Basic information

Entry
Database: PDB / ID: 4iwh
TitleCrystal structure of a 3-isopropylmalate dehydrogenase from Burkholderia pseudomallei
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / glyceraldehyde-3-phosphate / aconitase / GAPDH
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
3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a 3-isopropylmalate dehydrogenase from Burkholderia pseudomallei
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6804
Polymers78,6322
Non-polymers492
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-52 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.600, 60.100, 103.190
Angle α, β, γ (deg.)90.000, 112.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

21A-795-

HOH

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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 / Gene: BTH_II0674, leuB / Production host: Escherichia coli (E. coli)
References: UniProt: Q2T7H6, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ButhA.00092.a.B1 PS01671 at 23.6 mg/mL against MCSG1 screen condition d3, 0.2 M MgCl2, 0.1 M TrisHCl pH 8.5, 30% PEG 400, crystal tracking ID 240482d3, unique puck ID quk9-15, VAPOR ...Details: ButhA.00092.a.B1 PS01671 at 23.6 mg/mL against MCSG1 screen condition d3, 0.2 M MgCl2, 0.1 M TrisHCl pH 8.5, 30% PEG 400, crystal tracking ID 240482d3, unique puck ID quk9-15, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.283574 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283574 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 79884 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.078 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 24.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.264.6425700568295.8
1.8-1.840.2145.9527973577599.8
1.84-1.90.1946.6727256559999
1.9-1.960.1510.3123377535498
1.96-2.020.1131225714528899.3
2.02-2.090.08116.0425043511699.6
2.09-2.170.06719.0624260495199.8
2.17-2.260.06521.0220852468998
2.26-2.360.05723.0420819449298.2
2.36-2.470.04328.3621440438499.9
2.47-2.610.03831.9220367418699.8
2.61-2.770.03535.1119169393899.7
2.77-2.960.03239.0317951371799.5
2.96-3.20.02942.1516524344899.8
3.2-3.50.02845.8315063318499.6
3.5-3.910.02946.913036286599.1
3.91-4.520.02550.4311869257199.1
4.52-5.530.02352.4810573217499.6
5.53-7.830.02351.518221168499.4
7.830.02150.24345078780.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.62 Å
Translation3 Å19.62 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A05

1a05


Resolution: 1.75→19.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1966 / WRfactor Rwork: 0.1637 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8633 / SU B: 4.056 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1045 / SU Rfree: 0.1027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4014 5 %RANDOM
Rwork0.1676 ---
obs0.1693 79883 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.9 Å2 / Biso mean: 23.4711 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å2-0.36 Å2
2--0.18 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 2 799 6140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195526
X-RAY DIFFRACTIONr_bond_other_d0.0010.025324
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.987531
X-RAY DIFFRACTIONr_angle_other_deg0.807312268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41324.421233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15715902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9731535
X-RAY DIFFRACTIONr_chiral_restr0.0850.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021184
X-RAY DIFFRACTIONr_mcbond_it1.0231.6252884
X-RAY DIFFRACTIONr_mcbond_other1.021.6252883
X-RAY DIFFRACTIONr_mcangle_it1.5512.4343610
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 256 -
Rwork0.217 5418 -
all-5674 -
obs--95.78 %
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)
10.5222-0.16650.16710.0648-0.02510.20550.00690.0777-0.0246-0.026-0.00530.0105-0.05020.0911-0.00160.0492-0.0386-0.00840.0530.01050.0223.49260.763927.7038
20.31950.18960.05830.2137-0.04840.34350.0214-0.0124-0.02330.0708-0.01390.009-0.0532-0.0491-0.00750.04980.00090.01460.0119-0.0020.0201-30.02830.65121.8721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 355
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B1 - 355
4X-RAY DIFFRACTION2B401

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