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- PDB-4g07: The crystal structure of the C366S mutant of HDH from Brucella suis -

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Basic information

Entry
Database: PDB / ID: 4g07
TitleThe crystal structure of the C366S mutant of HDH from Brucella suis
ComponentsHistidinol dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / L-HISTIDINOL DEHYDROGENASE
Function / homology
Function and homology information


histidinol dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding / 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 speciesBrucella suis 1330 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsD'Ambrosio, K. / De Simone, G.
CitationJournal: Biochimie / Year: 2014
Title: Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis.
Authors: D'ambrosio, K. / Lopez, M. / Dathan, N.A. / Ouahrani-Bettache, S. / Kohler, S. / Ascione, G. / Monti, S.M. / Winum, J.Y. / De Simone, G.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4034
Polymers47,1801
Non-polymers2233
Water5,152286
1
A: Histidinol dehydrogenase
hetero molecules

A: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8068
Polymers94,3612
Non-polymers4466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area11030 Å2
ΔGint-150 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.672, 105.075, 112.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histidinol dehydrogenase / HDH


Mass: 47180.285 Da / Num. of mol.: 1 / Mutation: C366S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis 1330 (bacteria) / Strain: 1330 / Gene: hisD, BR0252, BS1330_I0253 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8G2R2, histidinol dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 25% PEG 3350, 0.1 M HEPES, 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 33309 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rsym value: 0.037 / Net I/σ(I): 46.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.36 / % possible all: 96.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1K75

1k75


Resolution: 1.95→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 1599 RANDOM
Rwork0.207 --
obs0.207 32306 -
all-33309 -
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 8 286 3525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→1.97 Å /
RfactorNum. reflection
Rfree0.364 53
Rwork0.304 -

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