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- PDB-1hqs: CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1hqs
TitleCRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM BACILLUS SUBTILIS
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / glyoxylate bypass / BsIDH / tricarboxylic acid cycle / protein phosphorylation / NADP
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / 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
CITRIC ACID / S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSingh, S.K. / Matsuno, K. / LaPorte, D.C. / Banaszak, L.J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase.
Authors: Singh, S.K. / Matsuno, K. / LaPorte, D.C. / Banaszak, L.J.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN Cys118 from both monomers have been modified with beta-mercaptoethanol.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE
B: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,00611
Polymers93,0892
Non-polymers9179
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-16 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.690, 73.290, 80.900
Angle α, β, γ (deg.)90.00, 109.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ISOCITRATE DEHYDROGENASE / OXALOSUCCINATE DECARBOXYLASE


Mass: 46544.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: CITC / Plasmid: PKM14 / Production host: Escherichia coli (E. coli) / Strain (production host): KME44
References: UniProt: P39126, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 23% PEG 4000, 18% propylene glycol, 0.1 M citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.9 mg/mlprotein1drop
2100 mMcitrate1reservoirpH4.9
323 %PEG40001reservoir
418 %propylene glycol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: APS-1 / Detector: CCD / Date: Feb 6, 1998 / Details: vertically focusing mirror
RadiationMonochromator: Sagitally focusing crystal/double crystal monochromator Si-111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→99 Å / Num. all: 244628 / Num. obs: 114797 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.13 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.321 / Num. unique all: 6004 / % possible all: 46.6
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 244628

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ICD

3icd


Resolution: 1.55→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used bulk-solvent correction. Citrate is bound in the active site of both monomers. However, the O5 and O6 atoms of the citrate bound in monomer B (res. number 825) have been set to zero to ...Details: Used bulk-solvent correction. Citrate is bound in the active site of both monomers. However, the O5 and O6 atoms of the citrate bound in monomer B (res. number 825) have been set to zero to account for a small negative peak (-3.4sigma) that appeared on them late in refinement. There are 23 pairs of water molecules less than 2.5-A apart enveloped in electron density that resembles a peanut shell or dumbbell. Their occupancies have been set to 0.5. In addition, there are 3 sets of water triplets less than 2.5-A apart enveloped in electron density that resembles a boomerang. Their occupancies have been set to 0.33. All 55 of these waters are appended at the end of the coordinate file. There is no visible electron density beyond the beta-carbon of Met1, Gln3, and Asn11 in monomer A. Their side chains were generated in O using the most common rotamers and their occupancies have been set to 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 5507 5 %RANDOM
Rwork0.202 ---
all-109218 --
obs-109218 92.9 %-
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-20 Å
Luzzati sigma a0.18 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 61 608 7445
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_mcbond_it1.441.5
X-RAY DIFFRACTIONx_mcangle_it2.182
X-RAY DIFFRACTIONx_scbond_it2.772
X-RAY DIFFRACTIONx_scangle_it4.462.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 704 5.4 %
Rwork0.326 12224 -
obs--66.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3cyc.paramCYC.TOPPAR
X-RAY DIFFRACTION4prgR.paramPRGR.TOPPAR
X-RAY DIFFRACTION5prgS.paramPRGS.TOPPAR
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.324 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.326

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