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- PDB-3orv: Crystal Structure of the Y294H-MauG/pre-Methylamine Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 3orv
TitleCrystal Structure of the Y294H-MauG/pre-Methylamine Dehydrogenase Complex
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein mauG
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / MauG / methylamine dehydrogenase / His-His heme / c-heme / quinone cofactor / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity ...methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily ...Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / 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 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
HEME C / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Methylamine dehydrogenase heavy chain / Methylamine dehydrogenase light chain / Methylamine utilization protein MauG
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsJensen, L.M.R. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2010
Title: Functional Importance of Tyrosine 294 and the Catalytic Selectivity for the Bis-Fe(IV) State of MauG Revealed by Replacement of This Axial Heme Ligand with Histidine .
Authors: Abu Tarboush, N. / Jensen, L.M. / Feng, M. / Tachikawa, H. / Wilmot, C.M. / Davidson, V.L.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Dec 27, 2023Group: Derived calculations / Category: struct_conn
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylamine utilization protein mauG
B: Methylamine utilization protein mauG
C: Methylamine dehydrogenase light chain
D: Methylamine dehydrogenase heavy chain
E: Methylamine dehydrogenase light chain
F: Methylamine dehydrogenase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,07322
Polymers197,1936
Non-polymers3,88016
Water23,4381301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26840 Å2
ΔGint-146 kcal/mol
Surface area59920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.527, 83.524, 107.782
Angle α, β, γ (deg.)109.94, 91.54, 105.78
Int Tables number1
Space group name H-MP1

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Components

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Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF

#1: Protein Methylamine utilization protein mauG


Mass: 41121.602 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 / Mutation: Y294H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauG / Production host: Paracoccus denitrificans (bacteria) / References: UniProt: Q51658, Oxidoreductases
#2: Antibody Methylamine dehydrogenase light chain


Mass: 15025.595 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188 / Mutation: Trp57 is hydroxylated at C7
Source method: isolated from a genetically manipulated source
Details: Immature MADH (preMADH) was produced in the absence of the mauG gene. Trp57 is monohydroxylated at the C7 position.
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauA / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22619, EC: 1.4.99.3
#3: Protein Methylamine dehydrogenase heavy chain


Mass: 42449.277 Da / Num. of mol.: 2 / Fragment: UNP residues 32-417
Source method: isolated from a genetically manipulated source
Details: Immature MADH (preMADH) was produced in the absence of the mauG gene. The alpha subunit has the wild-type sequence.
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4730 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3

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Non-polymers , 8 types, 1317 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1301 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / pH: 6.4
Details: Drops contained 1uL protein with 2uL reservoir solution. Protein solution: 100uM Y294H-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 24-26 % w/v PEG ...Details: Drops contained 1uL protein with 2uL reservoir solution. Protein solution: 100uM Y294H-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 24-26 % w/v PEG 8000, 0.1 M sodium acetate, 0.1 M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03325
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2009 / Details: BIOMORPH MIRRORS (KIRKPATRICK- BAEZ CONFIGURATION)
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03325 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 132062 / Num. obs: 126251 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.08 / Net I/σ(I): 13.6
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 6557 / Rsym value: 0.425 / % possible all: 70.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4M

3l4m


Resolution: 1.91→44.49 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.623 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS groups 1 and 2 include the amino acids, c-hemes (HEC ligands) and CA (calcium sites) ONLY (of residues 6-600) - at the exclusion of solvent and polyethylene glycol ligands
RfactorNum. reflection% reflectionSelection details
Rfree0.187 6318 5 %RANDOM BASED ON R-FREE FOR 3L4M
Rwork0.139 ---
obs0.141 119911 93.9 %-
all-127728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20.04 Å2-0.01 Å2
2--0.06 Å20.04 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13215 0 262 1301 14778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02213937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.97519011
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42751733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49723.7673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.957152061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.69615110
X-RAY DIFFRACTIONr_chiral_restr0.1920.21988
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111014
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_it1.1871.58558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.978213736
X-RAY DIFFRACTIONr_scbond_it3.31135379
X-RAY DIFFRACTIONr_scangle_it5.0234.55260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 264 -
Rwork0.234 5263 -
obs--55.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54920.1288-0.47410.4606-0.08432.1128-0.02810.0479-0.03460.01010.0087-0.0143-0.0252-0.05650.01940.10680.0150.0050.0343-0.04270.062421.77227.244-75.893
20.5958-0.07910.09820.674-0.51121.2302-0.0018-0.04180.0370.0685-0.02850.0033-0.0347-0.00030.03040.0277-0.01370.01290.036-0.01750.041724.24229.81423.16
30.6124-0.14890.0720.7843-0.09671.08880.00630.1241-0.0256-0.1564-0.00690.07630.1298-0.16540.00060.0831-0.0181-0.0110.0651-0.02170.03940.65429.142-47.599
40.3591-0.14690.07920.3742-0.01991.24210.0450.0205-0.1215-0.0871-0.01870.0880.4694-0.1646-0.02630.2254-0.0717-0.01690.03280.0030.12252.8419.708-29.56
50.55620.048-0.00280.3738-0.1840.7137-0.0054-0.08290.00450.01320.01170.03780.0553-0.0364-0.00630.0232-0.01060.01170.07230.01550.06942.11334.054-4.393
60.4317-0.0283-0.03210.39340.17240.52430.0173-0.01880.0627-0.0488-0.0189-0.0092-0.08460.00830.00170.0363-0.0040.00950.02260.00690.06117.94952.656-22.036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 600
2X-RAY DIFFRACTION2B6 - 600
3X-RAY DIFFRACTION3C7 - 130
4X-RAY DIFFRACTION4D11 - 386
5X-RAY DIFFRACTION5E7 - 130
6X-RAY DIFFRACTION6F11 - 386

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