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- PDB-2bbk: CRYSTAL STRUCTURE OF THE QUINOPROTEIN METHYLAMINE DEHYDROGENASE F... -

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Basic information

Entry
Database: PDB / ID: 2bbk
TitleCRYSTAL STRUCTURE OF THE QUINOPROTEIN METHYLAMINE DEHYDROGENASE FROM PARACOCCUS DENITRIFICANS AT 1.75 ANGSTROMS
Components
  • METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
  • METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain ...Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsChen, L. / Mathews, F.S.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Refined crystal structure of methylamine dehydrogenase from Paracoccus denitrificans at 1.75 A resolution.
Authors: Chen, L. / Doi, M. / Durley, R.C. / Chistoserdov, A.Y. / Lidstrom, M.E. / Davidson, V.L. / Mathews, F.S.
#1: Journal: Proteins / Year: 1992
Title: Three-Dimensional Structure of the Quinoprotein Methylamine Dehydrogenase from Paracoccus Denitrificans Determined by Molecular Replacement at 2.8 Angstroms Resolution
Authors: Chen, L. / Mathews, F.S. / Davidson, V.L. / Huizinga, E.G. / Vellieux, F.M.D. / Hol, W.G.J.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1992
Title: The Genetic Organization of the Mau Gene Cluster of the Facultative Autotroph Paracoccus Denitrificans
Authors: Chistoserdov, A.Y. / Boyd, J. / Mathews, F.S. / Lidstrom, M.E.
#3: Journal: FEBS Lett. / Year: 1991
Title: Crystallographic Investigations of the Tryptophan-Derived Cofactor in the Quinoprotein Methylamine Dehydrogenase
Authors: Chen, L. / Mathews, F.S. / Davidson, V.L. / Huizinga, E.G. / Vellieux, F.M.D. / Duine, J.A. / Hol, W.G.J.
#4: Journal: Embo J. / Year: 1989
Title: Structure of Quinoprotein Methylamine Dehydrogenase at 2.25 Angstroms Resolution
Authors: Vellieux, F.M.D. / Huitema, F. / Groendijk, H. / Kalk, K.H. / Frank Jzn., J. / Jongejan, J.A. / Duine, J.A. / Petratos, K. / Drenth, J. / Hol, W.G.J.
History
DepositionDec 17, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
J: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
M: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)106,2794
Polymers106,2794
Non-polymers00
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-39 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.070, 135.920, 55.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO H 145
2: PHE H 193 - GLY H 194 OMEGA =218.52 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO J 145
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9928, -0.0483, 0.1095), (-0.0405, -0.7257, -0.6868), (0.1127, -0.6863, 0.7186)
Vector: 119.012, 49.687, 12.331)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS H AND L WHEN APPLIED TO CHAINS J AND M, RESPECTIVELY.

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Components

#1: Protein METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)


Mass: 39411.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P29894, EC: 1.4.99.3
#2: Protein METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)


Mass: 13728.206 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P22619, EC: 1.4.99.3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE REDOX CENTERS OF MADH ARE LOCATED ON EACH L SUBUNIT. EACH IS COMPOSED OF THE SIDE CHAINS OF TWO ...THE REDOX CENTERS OF MADH ARE LOCATED ON EACH L SUBUNIT. EACH IS COMPOSED OF THE SIDE CHAINS OF TWO TRYPTOPHANS ON THE L SUBUNIT, LINKED BY COVALENT BOND BETWEEN TWO INDOLE RINGS. ONE INDOLE RING HAS AN ORTHO-QUINONE STRUCTURE. THIS DOUBLE-TRYPTOPHAN SYSTEM IS CALLED TRYPTOPHAN TRYPTOPHYL-QUINONE (TTQ). RESIDUE 57 OF CHAINS L AND M IS ACTUALLY TRYPTOPHYLQUINONE. THE ADDITIONAL OXYGEN ATOMS ARE PRESENTED AS RESIDUE OWQ AT THE END OF THE CHAINS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein solution1drop
21.8-2.0 Mammonium sulphate1dropunbuffered
31.8-2.0 Mammonium sulphate1reservoirunbuffered

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.75→11 Å / σ(F): 2.7
Details: THE SG ATOMS OF RESIDUES CYS L 23, CYS L 88, CYS M 23, AND CYS M 88 EACH ARE PRESENTED IN TWO ALTERNATE CONFORMATIONS. DURING REFINEMENT, THE OCCUPANCY WAS LEFT AT 1.0 FOR EACH CONFORMATION ...Details: THE SG ATOMS OF RESIDUES CYS L 23, CYS L 88, CYS M 23, AND CYS M 88 EACH ARE PRESENTED IN TWO ALTERNATE CONFORMATIONS. DURING REFINEMENT, THE OCCUPANCY WAS LEFT AT 1.0 FOR EACH CONFORMATION WHILE THE B VALUES WERE REFINED. IN THIS ENTRY, THE OCCUPANCY OF THESE ATOMS HAS BEEN SET ARBITRARILY TO 0.5.
RfactorNum. reflection
obs0.167 111755
Refinement stepCycle: LAST / Resolution: 1.75→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 0 556 8038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 11 Å / Num. reflection obs: 111755 / σ(F): 2.7 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d16.913
X-RAY DIFFRACTIONt_plane_restr0.02

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