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- PDB-6xxy: Crystal structure of Haemophilus influenzae 3-isopropylmalate deh... -

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Basic information

Entry
Database: PDB / ID: 6xxy
TitleCrystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with O-isobutenyl oxalylhydroxamate.
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / Haemophilus influenzae / leucine biosynthetis / 3-isopropylmalate dehydrogenase / inhibitor
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytosol
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 / Chem-O45 / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMiggiano, R. / Rossi, F. / Martignon, S. / Rizzi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase (LeuB) in complex with the inhibitor O-isobutenyl oxalylhydroxamate.
Authors: Miggiano, R. / Martignon, S. / Minassi, A. / Rossi, F. / Rizzi, M.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
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_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,3888
Polymers77,6952
Non-polymers1,6946
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-63 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.936, 116.936, 92.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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


Mass: 38847.324 Da / Num. of mol.: 2 / Mutation: Q2E
Source method: isolated from a genetically manipulated source
Details: Glutammic acid at residue 2 has been introduced as result of subcloning strategies
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: leuB, HI_0987 / Production host: Escherichia coli (E. coli)
References: UniProt: P43860, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-O45 / 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid


Mass: 159.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2 M (NH4)2SO4, 0.1 M Na-citrate pH 5.5 and 5% 2-propanol.

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.09→58.49 Å / Num. obs: 41922 / % possible obs: 98.53 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.053 / Net I/σ(I): 12.75
Reflection shellResolution: 2.09→2.39 Å / Rmerge(I) obs: 0.2037 / Mean I/σ(I) obs: 4.59 / Num. unique obs: 3733

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
REFMAC1.13_2998refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A05

1a05


Resolution: 2.09→58.49 Å / SU ML: 0.2852 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8791
RfactorNum. reflection% reflection
Rfree0.2277 432 1.03 %
Rwork0.1817 --
obs0.1821 41922 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.55 Å2
Refinement stepCycle: LAST / Resolution: 2.09→58.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 112 353 5913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00765669
X-RAY DIFFRACTIONf_angle_d1.03357681
X-RAY DIFFRACTIONf_chiral_restr0.0552854
X-RAY DIFFRACTIONf_plane_restr0.0053997
X-RAY DIFFRACTIONf_dihedral_angle_d14.29723413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.390.27391460.203713414X-RAY DIFFRACTION95.97
2.39-3.010.26951300.205814023X-RAY DIFFRACTION99.99
3.01-58.470.19851560.163914053X-RAY DIFFRACTION99.34

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