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- PDB-4y5r: Crystal Structure of a T67A MauG/pre-Methylamine Dehydrogenase Complex -

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Basic information

Entry
Database: PDB / ID: 4y5r
TitleCrystal Structure of a T67A MauG/pre-Methylamine Dehydrogenase Complex
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein MauG
KeywordsOXIDOREDUCTASE / MauG / Heme / 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 / Methylamine dehydrogenase heavy chain / Methylamine dehydrogenase light chain / Methylamine utilization protein MauG
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsLi, C. / Wilmot, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: A T67A mutation in the proximal pocket of the high-spin heme of MauG stabilizes formation of a mixed-valent Fe(II)/Fe(III) state and enhances charge resonance stabilization of the bis-Fe(IV) state.
Authors: Shin, S. / Feng, M. / Li, C. / Williamson, H.R. / Choi, M. / Wilmot, C.M. / Davidson, V.L.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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)190,69212
Polymers188,1386
Non-polymers2,5546
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24280 Å2
ΔGint-181 kcal/mol
Surface area59860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.530, 83.520, 107.780
Angle α, β, γ (deg.)109.940, 91.540, 105.780
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: 38946.277 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-380 / Mutation: T67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: mauG, Pden_4736 / Production host: Paracoccus denitrificans PD1222 (bacteria) / References: UniProt: Q51658, Oxidoreductases
#2: Antibody Methylamine dehydrogenase light chain / MADH / Methylamine dehydrogenase (amicyanin)


Mass: 13714.224 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 64-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: mauA / Production host: Rhodobacter sphaeroides (bacteria)
References: UniProt: P22619, methylamine dehydrogenase (amicyanin)
#3: Protein Methylamine dehydrogenase heavy chain


Mass: 41408.266 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 42-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_4730 / Production host: Rhodobacter sphaeroides (bacteria)
References: UniProt: A1BB97, methylamine dehydrogenase (amicyanin)

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Non-polymers , 3 types, 12 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 25-30% PEG 8000, 0,1 M sodium Acetate, 0.1 M MES pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.003 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 23, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.58→29.61 Å / Num. obs: 51683 / % possible obs: 95.2 % / Redundancy: 1.9 % / CC1/2: 0.902 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.111 / Net I/σ(I): 5.2 / Num. measured all: 98206
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.58-2.661.80.6391.2562931150.4370.63966
10.62-29.611.90.02111.613797200.9970.02193.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3L4M

3l4m


Resolution: 2.8→29.61 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.855 / SU B: 37.461 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 2135 5.1 %RANDOM
Rwork0.1932 39834 --
obs0.1964 39834 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.79 Å2 / Biso mean: 51.054 Å2 / Biso min: 26.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.27 Å20.9 Å2
2--0.51 Å20.68 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.8→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13227 0 174 6 13407
Biso mean--41.86 40.41 -
Num. residues----1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913812
X-RAY DIFFRACTIONr_bond_other_d00.0212538
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.97218883
X-RAY DIFFRACTIONr_angle_other_deg3.712328847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72451717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96523.772668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.515152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.94715106
X-RAY DIFFRACTIONr_chiral_restr0.0790.21978
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116057
X-RAY DIFFRACTIONr_gen_planes_other0.0130.023249
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 167 -
Rwork0.259 2908 -
all-3075 -
obs--98.02 %
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)
10.22230.0964-0.26290.1-0.04160.7083-0.0034-0.0028-0.01950.0013-0.0009-0.0041-0.03810.00290.00440.11140.0586-0.03530.0574-0.04950.049921.649727.3432-76.0111
20.3590.05550.00560.3126-0.36060.64010.0303-0.01880.00290.0387-0.03230.0156-0.03230.05140.00210.09210.0224-0.02490.0407-0.0360.038524.129629.851523.1926
30.13440.2124-0.01480.42610.14870.43210.00350.0022-0.0171-0.069-0.03210.0009-0.0332-0.03690.02860.11570.0763-0.05380.0666-0.04940.03880.688128.675-47.9548
40.1052-0.04620.06790.2453-0.03040.51580.02950.0085-0.0226-0.0178-0.00650.01430.1488-0.0566-0.0230.10940.007-0.0580.0239-0.03220.07122.52139.1163-29.7754
50.0034-0.03560.03590.3795-0.38020.3895-0.0001-0.004-0.00180.01580.04290.0180.001-0.029-0.04280.06440.0402-0.02990.04-0.03440.08762.371233.9424-3.9208
60.1697-0.0596-0.0020.2770.15640.20390.0068-0.01710.0359-0.04170.0004-0.0157-0.0445-0.0042-0.00720.07780.0374-0.02560.0299-0.03740.06327.992152.5807-22.2458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999

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