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- PDB-3svw: Crystal Structure of the P107V-MauG/pre-Methylamine Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 3svw
TitleCrystal Structure of the P107V-MauG/pre-Methylamine Dehydrogenase Complex
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein MauG
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / MauG / methylamine dehydrogenase / 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, L chain ...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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / HEME C / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Methylamine dehydrogenase heavy chain / Methylamine dehydrogenase (amicyanin) / Methylamine dehydrogenase light chain / Methylamine utilization protein MauG
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsJensen, L.M.R. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2012
Title: Proline 107 is a major determinant in maintaining the structure of the distal pocket and reactivity of the high-spin heme of MauG.
Authors: Feng, M. / Jensen, L.M. / Yukl, E.T. / Wei, X. / Liu, A. / Wilmot, C.M. / Davidson, V.L.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)200,80225
Polymers197,2476
Non-polymers3,55519
Water37,9582107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26720 Å2
ΔGint-196 kcal/mol
Surface area59410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.606, 89.001, 104.812
Angle α, β, γ (deg.)67.05, 79.51, 79.72
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: 41148.645 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 / Mutation: P107V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauG, Pden_4736 / Production host: Paracoccus denitrificans (bacteria) / References: UniProt: Q51658, Oxidoreductases
#2: Antibody Methylamine dehydrogenase light chain / MADH / The beta subunit of immature methylamine dehydrogenase (preMADH)


Mass: 15025.595 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188
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, UniProt: A1BBA0*PLUS, EC: 1.4.99.3
#3: Protein Methylamine dehydrogenase heavy chain / The alpha subunit of immature methylamine dehydrogenase (preMADH)


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 , 9 types, 2126 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-HEC / HEME C


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2107 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM P107V-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 23% w/v PEG ...Details: Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM P107V-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 23% w/v PEG 8000, 0.1M sodium acetate, 0.1M 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-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2011 / 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 149957 / Num. obs: 145458 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rsym value: 0.039 / Net I/σ(I): 21.1
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7.7 / Num. unique all: 7530 / Rsym value: 0.118 / % possible all: 86.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4M

3l4m


Resolution: 1.86→33.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.965 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17433 7327 5 %RANDOM
Rwork0.13136 ---
obs0.13355 138130 96.19 %-
all-143601 --
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: 19.366 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13179 0 237 2107 15523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02213944
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.97219052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35551739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97723.658678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41152075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71815110
X-RAY DIFFRACTIONr_chiral_restr0.2040.21996
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111050
X-RAY DIFFRACTIONr_mcbond_it1.1781.58542
X-RAY DIFFRACTIONr_mcangle_it1.893213725
X-RAY DIFFRACTIONr_scbond_it3.06735402
X-RAY DIFFRACTIONr_scangle_it4.6894.55304
LS refinement shellResolution: 1.862→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 428 -
Rwork0.154 8291 -
obs--78.39 %
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)
10.3155-0.03190.17670.2852-0.260.9043-0.03630.0073-0.0011-0.00060.0249-0.0232-0.04190.00640.01150.0467-0.02260.01410.0305-0.03260.038921.1022-35.182471.8008
20.3179-0.12030.03280.6486-0.68671.06120.01960.0011-0.008-0.1038-0.03680.00430.10290.02050.01720.02440.007-0.01220.0184-0.00980.021224.1463-27.7111-26.1088
30.3158-0.0583-0.17310.21510.07920.49040.0181-0.01260.0180.0568-0.01010.0313-0.0497-0.0161-0.0080.0442-0.00250.02210.0373-0.01360.02590.0424-32.997544.6566
40.15160.0826-0.02390.11570.04840.63640.03880.01320.08330.0312-0.01130.0387-0.2394-0.0374-0.02750.11240.00930.02410.00660.01180.06762.6073-12.612327.6906
50.10410.05040.03570.2213-0.12170.34120.00640.05250.0227-0.00930.04620.0501-0.0346-0.0161-0.05260.01650.0034-0.01330.06990.0250.07151.8294-34.90840.6421
60.17060.0357-0.02650.23570.12140.41170.00780.0232-0.0250.03170.00760.0120.05630.0027-0.01540.01290.0017-0.01360.03370.00130.0437.6678-55.049816.6126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 359
2X-RAY DIFFRACTION2B6 - 360
3X-RAY DIFFRACTION3C7 - 137
4X-RAY DIFFRACTION4D11 - 386
5X-RAY DIFFRACTION5E7 - 131
6X-RAY DIFFRACTION6F11 - 386

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