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- PDB-1k75: The L-histidinol dehydrogenase (hisD) structure implicates domain... -

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Basic information

Entry
Database: PDB / ID: 1k75
TitleThe L-histidinol dehydrogenase (hisD) structure implicates domain swapping and gene duplication.
ComponentsL-histidinol dehydrogenase
KeywordsOXIDOREDUCTASE / L-histidinol dehydrogenase / homodimer / Rossmann fold / 4 domains / hisD / L-histidine biosynthesis / NAD cofactor / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


histidinol dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / manganese ion binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Nitrogenase molybdenum iron protein domain / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Nitrogenase molybdenum iron protein domain / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histidinol dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsBarbosa, J.A.R.G. / Sivaraman, J. / Li, Y. / Larocque, R. / Matte, A. / Schrag, J. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase.
Authors: Barbosa, J.A.R.G. / Sivaraman, J. / Li, Y. / Larocque, R. / Matte, A. / Schrag, J.D. / Cygler, M.
History
DepositionOct 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-histidinol dehydrogenase
B: L-histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3457
Polymers92,8692
Non-polymers4765
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-107 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.370, 107.520, 157.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological (functional) hisD is the homodimer in the assymetric unit. No symmetry operations are needed.

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Components

#1: Protein L-histidinol dehydrogenase


Mass: 46434.520 Da / Num. of mol.: 2 / Fragment: Se-Met derived dimer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hisD / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P06988, histidinol dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, glycerol, imidazole/malic acid buffer, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115.4 mg/mlprotein1drop
220 mMTris-Cl1droppH7.5
30.2 M1dropNaCl
45 mMdithiothreitol1drop
51 mML-histidine1drop
620 %(w/v)PEG33501reservoir
77 %(v/v)glycerol1reservoir
80.1 Mimidazole-malic acid1reservoirpH5.5
90.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97950,0.97934,0.97857
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2000 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979341
30.978571
ReflectionResolution: 1.75→40 Å / Num. all: 91930 / Num. obs: 91930 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3675 / Rsym value: 0.276 / % possible all: 79.7
Reflection
*PLUS
Num. obs: 91330 / Num. measured all: 402344 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 79.7 % / Rmerge(I) obs: 0.276

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2241 -random
Rwork0.19 ---
all-88622 --
obs-88622 96.9 %-
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.92 Å2-2.62 Å2-5.3 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 26 924 7370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_deg22.4
X-RAY DIFFRACTIONc_improper_deg1.06
X-RAY DIFFRACTIONc_mcbond_it1.33
X-RAY DIFFRACTIONc_mcangle_it1.94
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.262 184 -
Rwork0.244 --
obs-6819 73.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.33
X-RAY DIFFRACTIONc_mcangle_it1.94
LS refinement shell
*PLUS
Lowest resolution: 1.78 Å / Rfactor Rwork: 0.244 / Rfactor obs: 0.244

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