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- PDB-3k30: Histamine dehydrogenase from Nocardiodes simplex -

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Basic information

Entry
Database: PDB / ID: 3k30
TitleHistamine dehydrogenase from Nocardiodes simplex
ComponentsHistamine dehydrogenase
KeywordsOXIDOREDUCTASE / 6-S-cysteinyl-FMN / ADP binding site
Function / homology
Function and homology information


FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I ...Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / Histamine dehydrogenase
Similarity search - Component
Biological speciesPimelobacter simplex (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsScott, E.E. / Reed, T.M. / Limburg, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of histamine dehydrogenase from Nocardioides simplex.
Authors: Reed, T. / Lushington, G.H. / Xia, Y. / Hirakawa, H. / Travis, D.M. / Mure, M. / Scott, E.E. / Limburg, J.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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

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Assembly

Deposited unit
A: Histamine dehydrogenase
B: Histamine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,7838
Polymers151,3132
Non-polymers2,4706
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-82 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.141, 107.035, 153.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological homodimer in the asymmetric unit

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Components

#1: Protein Histamine dehydrogenase


Mass: 75656.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pimelobacter simplex (bacteria) / Strain: ATCC 6946 / Gene: hadh, hdh / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q6IWJ5
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS THIS MAY BE EITHER A POLYMORPHISM OR A SEQUENCING ERROR AT THE UNP ...ACCORDING TO THE AUTHORS THIS MAY BE EITHER A POLYMORPHISM OR A SEQUENCING ERROR AT THE UNP DATABASE. THE DENSITY CONFIRMS ALA AT POSITION 615.

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 0.1 HEPES buffer (pH 7.4) containing 2.0 M (NH4)2SO4 and 2% 400-PEG (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→84.5 Å / Num. obs: 46309 / % possible obs: 99.7 % / Redundancy: 9.7 %
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 6.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DJN

1djn


Resolution: 2.7→84.43 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.341 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 1.51 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2336 5.1 %RANDOM
Rwork0.182 ---
obs0.185 43913 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→84.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10544 0 132 8 10684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.97314850
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34251366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98122.957514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.641151732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.71915120
X-RAY DIFFRACTIONr_chiral_restr0.1140.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7241.56774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.424210866
X-RAY DIFFRACTIONr_scbond_it2.4234132
X-RAY DIFFRACTIONr_scangle_it4.0884.53960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 168 -
Rwork0.232 3143 -
obs--98.6 %

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