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- PDB-3l4o: Crystal Structure of the MauG/pre-Methylamine Dehydrogenase Compl... -

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Basic information

Entry
Database: PDB / ID: 3l4o
TitleCrystal Structure of the MauG/pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide
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 / Difference Fourier / molecular replacement / Resolution: 2.046 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 / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)200,31715
Polymers197,2716
Non-polymers3,0469
Water22,8431268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24720 Å2
ΔGint-186 kcal/mol
Surface area60400 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: 15039.577 Da / Num. of mol.: 2
Fragment: Beta chain of immature methylamine dehydrogenase (preMADH)
Mutation: Hydroxylated Trp57 has been converted to the full-quinone form due to hydrogen peroxide-assisted catalysis by MauG in the crystal.
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, 1277 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.: 1268 / 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: 46.32 %
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; followed by reaction of the crystal with hydrogen peroxide immediately prior to flash cooling., 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: Aug 17, 2009 / Details: BIOMORPH MIRRORS (KIRKPATRICK-BAEZ CONFIGURATION)
RadiationMonochromator: Si(111) Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 123424 / Num. obs: 120574 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 36.09 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Χ2: 1.042 / Net I/σ(I): 17.1
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5673 / Χ2: 1.096 / % possible all: 92.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Difference Fourier
Starting model: 3l4m

3l4m


Resolution: 2.046→38.2 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.146 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.883 / SU B: 8.088 / SU ML: 0.105 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5304 5 %RANDOM
Rwork0.142 ---
obs0.145 106312 97.02 %-
all-109575 --
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: 69.61 Å2 / Biso mean: 21.828 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.07 Å20.06 Å2
2--0.05 Å2-0.02 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.046→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 207 1268 14703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02213842
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.97418893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72251712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06723.782669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.441152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.44815106
X-RAY DIFFRACTIONr_chiral_restr0.1380.21976
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110972
X-RAY DIFFRACTIONr_mcbond_it1.0361.58535
X-RAY DIFFRACTIONr_mcangle_it1.716213683
X-RAY DIFFRACTIONr_scbond_it2.96335307
X-RAY DIFFRACTIONr_scangle_it4.424.55206
LS refinement shellResolution: 2.046→2.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 318 -
Rwork0.183 6327 -
all-6645 -
obs-6645 82.3 %
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)
10.75180.2231-0.53890.4799-0.06271.7572-0.1030.0979-0.09850.01990.0351-0.0480.0664-0.07110.06790.12180.0202-0.00710.0455-0.05670.081621.78427.241-75.92
20.8193-0.03340.01050.7877-0.75021.5836-0.0007-0.09720.0460.0992-0.02850.007-0.0560.03160.02930.02450.00020.00040.0275-0.0240.032424.35630.06823.041
30.2798-0.1362-0.01250.8885-0.44281.35980.01880.0825-0.0471-0.24320.00470.08480.2316-0.2131-0.02350.097-0.0132-0.04260.0811-0.020.04070.66928.96-47.572
40.3087-0.0471-0.15720.6132-0.40561.7514-0.01320.0086-0.1191-0.22920.02220.09250.6176-0.2384-0.0090.2411-0.0825-0.03870.03660.0090.12472.7099.809-29.306
50.3519-0.0716-0.07060.6033-0.28330.67290.0138-0.05580.01110.02960.01050.03020.0049-0.0289-0.02430.0043-0.0068-0.00140.08690.02370.08222.32634.254-4.23
60.4676-0.0635-0.05910.49860.10820.75850.0317-0.02180.0751-0.0594-0.0279-0.0043-0.1210.0247-0.00390.0265-0.0048-0.00320.02450.01530.07027.88452.686-22.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 359
2X-RAY DIFFRACTION2B7 - 360
3X-RAY DIFFRACTION3C7 - 131
4X-RAY DIFFRACTION4D11 - 386
5X-RAY DIFFRACTION5E7 - 131
6X-RAY DIFFRACTION6F11 - 386

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