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- PDB-4o1q: Crystal Structure of the Q103N-MauG/pre-Methylamine Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4o1q
TitleCrystal Structure of the Q103N-MauG/pre-Methylamine Dehydrogenase Complex
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein MauG
KeywordsOXIDOREDUCTASE
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 / 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
HEME C / TRIETHYLENE GLYCOL / PHOSPHATE ION / Methylamine dehydrogenase heavy chain / Methylamine dehydrogenase (amicyanin) / Methylamine utilization protein MauG
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.59 Å
AuthorsYukl, E.T. / Wilmot, C.W.
CitationJournal: Biochemistry / Year: 2014
Title: Site-directed mutagenesis of Gln103 reveals the influence of this residue on the redox properties and stability of MauG.
Authors: Shin, S. / Yukl, E.T. / Sehanobish, E. / Wilmot, C.M. / Davidson, V.L.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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 1.2Dec 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)200,35820
Polymers196,9596
Non-polymers3,39914
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25700 Å2
ΔGint-177 kcal/mol
Surface area58270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.530, 83.520, 107.780
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: 41132.613 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 / Mutation: Q103N
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


Mass: 15025.597 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4733 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BBA0, EC: 1.4.99.3
#3: Protein Methylamine dehydrogenase heavy chain


Mass: 42321.152 Da / Num. of mol.: 2 / Fragment: UNP residues 33-417
Source method: isolated from a genetically manipulated source
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, 411 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M MES, pH 6.4, 0.1 M sodium acetate, 24-30% w/v PEG8000, 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: 1.03324 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 54052 / Num. obs: 53091 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 12.375
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.13 / Rsym value: 0.599 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CBASSdata collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3L4M

3l4m


Resolution: 2.59→44.49 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 29.95 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25423 2653 5 %RANDOM
Rwork0.19781 ---
all0.20066 51362 --
obs0.20066 50437 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.599 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å21.05 Å2-0.5 Å2
2--4.28 Å22.3 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.59→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13231 0 226 397 13854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01913877
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212614
X-RAY DIFFRACTIONr_angle_refined_deg1.41.97618973
X-RAY DIFFRACTIONr_angle_other_deg0.7633.00129022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6851715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8623.791670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.861152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.37715106
X-RAY DIFFRACTIONr_chiral_restr0.0920.21991
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116081
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023245
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 166 -
Rwork0.309 3621 -
obs--93.64 %
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)
11.4530.371-0.42360.7306-0.65163.03470.01250.2048-0.0934-0.08450.0288-0.02950.25690.1301-0.04140.61910.10220.05290.213-0.29990.541821.745428.0068-76.7039
20.93570.1678-0.22031.2891-1.19553.05030.0104-0.06190.08150.152-0.08840.0085-0.13350.17660.0780.4069-0.02770.10060.131-0.21450.410923.977629.294323.6824
31.495-0.09130.29641.6686-1.68013.27970.21470.2469-0.2252-0.36460.10230.23750.4776-0.3161-0.3170.5034-0.04090.00690.1675-0.18560.43690.911229.0634-48.2312
40.4128-0.0690.04090.6816-0.69962.00260.10440.0275-0.2261-0.30440.17030.12980.7729-0.3525-0.27470.6232-0.1779-0.09890.1422-0.13140.53352.829410.1442-30.3745
51.735-0.3209-0.16261.0959-0.57471.13110.088-0.1876-0.01770.03650.08090.1197-0.0272-0.0999-0.16880.1692-0.03720.08020.1016-0.10640.26072.473533.8094-3.6189
60.4828-0.03690.07470.7625-0.26361.65690.0467-0.05720.10290.01080.02570.0348-0.2512-0.1576-0.07240.3310.00110.12220.1037-0.17310.38457.867551.7638-21.7693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 359
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION2B6 - 360
4X-RAY DIFFRACTION2B401 - 403
5X-RAY DIFFRACTION3C7 - 131
6X-RAY DIFFRACTION4D11 - 386
7X-RAY DIFFRACTION5E7 - 131
8X-RAY DIFFRACTION6F11 - 386

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