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- PDB-4l3h: Crystal Structure of the E113Q-MauG/pre-Methylamine Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4l3h
TitleCrystal Structure of the E113Q-MauG/pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein MauG
KeywordsOXIDOREDUCTASE / electron transfer
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 / electron transfer activity / periplasmic space ...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 / electron transfer activity / periplasmic space / 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 / TRIETHYLENE GLYCOL / 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: 1.79 Å
AuthorsYukl, E.T. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2013
Title: Carboxyl Group of Glu113 Is Required for Stabilization of the Diferrous and Bis-Fe(IV) States of MauG.
Authors: Abu Tarboush, N. / Yukl, E.T. / Shin, S. / Feng, M. / Wilmot, C.M. / Davidson, V.L.
History
DepositionJun 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 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_alt_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_alt_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_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_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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)200,42023
Polymers196,9856
Non-polymers3,43517
Water26,4101466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25910 Å2
ΔGint-193 kcal/mol
Surface area58480 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: 41145.645 Da / Num. of mol.: 2 / Mutation: E113Q
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: 15025.595 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 spheroides (bacteria) / References: UniProt: A1BBA0, EC: 1.4.99.3
#3: Protein Methylamine dehydrogenase heavy chain


Mass: 42321.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4730 / Production host: Rhodobacter spheroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3

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Non-polymers , 7 types, 1483 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: 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
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1466 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
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-D / Wavelength: 1.03313 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 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: 1.03313 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 168632 / Num. obs: 162378 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.97
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.17 / % possible all: 83.8

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Processing

Software
NameVersionClassification
Blu-Icedata 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: 1.79→44.49 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.765 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19815 7881 5 %RANDOM
Rwork0.1542 ---
all0.1564 155541 --
obs0.1564 150844 96.98 %-
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: 39.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20.06 Å20.11 Å2
2---0.13 Å20.08 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.79→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13288 0 228 1466 14982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01914248
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212949
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.97719471
X-RAY DIFFRACTIONr_angle_other_deg0.9363.00229768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9251772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93223.719691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.856152109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.31215113
X-RAY DIFFRACTIONr_chiral_restr0.1440.22021
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02116592
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023365
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 569 -
Rwork0.258 10400 -
obs--90.94 %
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)
10.3702-0.24270.11050.4744-0.24980.94670.15090.0078-0.0666-0.15860.01980.15340.2028-0.0848-0.17080.146-0.0658-0.05310.06120.01280.10984.3831.0817-26.2134
20.41440.424-0.31560.5196-0.32382.1474-0.0279-0.005-0.0045-0.02750.0728-0.09690.32070.2896-0.04490.30050.1249-0.05030.1356-0.10410.111621.683227.7065-76.5104
30.6150.0131-0.12130.807-0.8611.9099-0.0049-0.10240.02210.1451-0.01260.0034-0.1501-0.04830.01740.0994-0.05860.04550.0702-0.04540.039823.969729.633923.4335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C7 - 135
2X-RAY DIFFRACTION1D11 - 386
3X-RAY DIFFRACTION1E7 - 131
4X-RAY DIFFRACTION1F11 - 386
5X-RAY DIFFRACTION2A6 - 359
6X-RAY DIFFRACTION2A401 - 403
7X-RAY DIFFRACTION3B6 - 362
8X-RAY DIFFRACTION3B401 - 403

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