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- PDB-3l4m: Crystal Structure of the MauG/pre-Methylamine Dehydrogenase Complex. -

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Basic information

Entry
Database: PDB / ID: 3l4m
TitleCrystal Structure of the MauG/pre-Methylamine Dehydrogenase Complex.
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein mauG
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / MauG / methylamine dehydrogenase / quinone cofactor / TTQ / His-Tyr heme / Electron transport / c-heme / Iron / Metal-binding / Oxidoreductase / Transport / Disulfide bond / 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 / 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 / molecular replacement / Resolution: 2.02 Å
AuthorsJensen, L.M.R. / Wilmot, C.M.
CitationJournal: Science / Year: 2010
Title: In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex.
Authors: Jensen, L.M. / Sanishvili, R. / Davidson, V.L. / Wilmot, C.M.
History
DepositionDec 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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.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 1.4Nov 22, 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)200,28915
Polymers197,2436
Non-polymers3,0469
Water23,4921304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24740 Å2
ΔGint-186 kcal/mol
Surface area60330 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: 41146.629 Da / Num. of mol.: 2
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 / MADH


Mass: 15025.595 Da / Num. of mol.: 2
Fragment: Beta chain of immature methylamine dehydrogenase (preMADH)
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, UniProt: A1BBA0*PLUS, EC: 1.4.99.3
#3: Protein Methylamine dehydrogenase heavy chain


Mass: 42449.277 Da / Num. of mol.: 2
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 , 6 types, 1313 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1304 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M MES pH 6.4, 0.1M sodium acetate, 24-30 % w/v PEG 8000, 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: 1.02665 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2008 / 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: 1.02665 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 113264 / Num. obs: 105427 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 27.03 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 10.74
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.3 / Num. unique all: 11318 / % possible all: 68.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mda, 1iqc

1mda

1iqc


Resolution: 2.02→44.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.149 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.893 / SU B: 7.499 / SU ML: 0.094 / SU R Cruickshank DPI: 0.171 / SU Rfree: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSTIONS. U VALUES: RESIDUAL ONLY. The MADH model (1MDA) did not provide sufficient phasing to determine the structures of the MauG copies. The ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSTIONS. U VALUES: RESIDUAL ONLY. The MADH model (1MDA) did not provide sufficient phasing to determine the structures of the MauG copies. The Chainsaw software within the CCP4i suite was used to reduce the CCP (1IQC) input (following sequence alignment with MauG) such that only strictly conserved residues near heme sites or else with secondary structure (alpha-helix) were retained as the input model. The missing MauG residues were added in an iterative manner by placing residues at termini of the discontinuous model peptide chains (as appropriate according to the electron-density map) and refining with successively more residues located for MauG.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 5298 5 %RANDOM
Rwork0.135 ---
all0.138 113788 --
obs0.138 105423 92.65 %-
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 max: 60.58 Å2 / Biso mean: 15.169 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0.01 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.02→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13231 0 207 1304 14742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02213850
X-RAY DIFFRACTIONr_angle_refined_deg2.021.97418909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4851717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17623.772668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.336152046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.32315106
X-RAY DIFFRACTIONr_chiral_restr0.1780.21980
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110978
X-RAY DIFFRACTIONr_mcbond_it1.1041.58547
X-RAY DIFFRACTIONr_mcangle_it1.922213705
X-RAY DIFFRACTIONr_scbond_it3.2335303
X-RAY DIFFRACTIONr_scangle_it5.0094.55198
LS refinement shellResolution: 2.021→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 248 -
Rwork0.157 4872 -
all-5120 -
obs--60.44 %
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)
10.3473-0.0604-0.01850.32370.14190.5580.0174-0.02830.0442-0.0516-0.0076-0.0076-0.07330.0208-0.00980.0194-0.0050.00990.01550.01020.04537.89352.298-22.165
20.4283-0.1615-0.11570.4439-0.21950.5015-0.0138-0.0651-0.00010.02520.03290.01540.03210.0055-0.01920.0103-0.00190.00870.05640.01740.05162.37633.657-4.146
30.3215-0.1045-0.00380.3836-0.10050.84420.04110.0058-0.0952-0.08390.00080.090.2794-0.0979-0.04190.1095-0.0337-0.03190.01950.01890.08452.7219.435-30.036
40.45510.09150.12310.819-0.18630.70710.00560.0535-0.0141-0.13940.03340.07630.0824-0.0745-0.03910.032-0.0029-0.02160.0313-0.00680.01920.76128.821-47.893
50.65820.0032-0.01430.6725-0.66631.32550.0228-0.08660.05860.0829-0.04750.0143-0.05460.01390.02470.0237-0.00870.01140.0216-0.01640.019424.31430.01523.156
60.46860.1576-0.32740.4165-0.18251.4992-0.0460.0486-0.0409-0.00740.0096-0.0364-0.0087-0.0440.03640.04590.0238-0.00450.032-0.02410.03921.84727.266-76.084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F12 - 386
2X-RAY DIFFRACTION2E7 - 130
3X-RAY DIFFRACTION3D12 - 386
4X-RAY DIFFRACTION4C7 - 130
5X-RAY DIFFRACTION5B8 - 360
6X-RAY DIFFRACTION6A8 - 359

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