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- PDB-3sle: Crystal Structure of the P107C-MauG/pre-Methylamine Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 3sle
TitleCrystal Structure of the P107C-MauG/pre-Methylamine Dehydrogenase Complex
Components
  • (Methylamine dehydrogenase ...) x 2
  • Methylamine utilization protein MauG
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Oxidoreductase / 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 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
ACETATE ION / 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: 2.52 Å
AuthorsYukl, E.T. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2012
Title: Proline 107 is a major determinant in maintaining the structure of the distal pocket and reactivity of the high-spin heme of MauG.
Authors: Feng, M. / Jensen, L.M. / Yukl, E.T. / Wei, X. / Liu, A. / Wilmot, C.M. / Davidson, V.L.
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Structure summary
Revision 1.2Sep 13, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)199,97718
Polymers197,0636
Non-polymers2,91412
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-177 kcal/mol
Surface area59830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.851, 88.530, 107.698
Angle α, β, γ (deg.)116.21, 91.83, 99.35
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLUGLUAA6 - 3596 - 359
21ALAALAGLUGLUBB6 - 3596 - 359
12THRTHRSERSERCC7 - 1317 - 131
22THRTHRSERSEREE7 - 1317 - 131
13GLNGLNGLYGLYDD11 - 38610 - 385
23GLNGLNGLYGLYFF11 - 38610 - 385

NCS ensembles :
ID
1
2
3

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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: 41184.656 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 / Mutation: P107C
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 / MADH


Mass: 15025.595 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188
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, EC: 1.4.99.3
#3: Protein Methylamine dehydrogenase heavy chain / MADH


Mass: 42321.152 Da / Num. of mol.: 2 / Fragment: UNP residues 32-417
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: mauB, pden_4730 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3

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Non-polymers , 5 types, 400 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 48.23 %
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, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2010 / 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 61043 / Num. obs: 59309 / % possible obs: 97.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.85
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.44 / % possible all: 94.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3L4M

3l4m


Resolution: 2.52→47.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / SU B: 25.785 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 2.287 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24339 2992 5 %RANDOM
Rwork0.17445 ---
obs0.17792 56313 96.89 %-
all-61043 --
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 mean: 52.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-2.2 Å2-1.21 Å2
2--4.3 Å23.46 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.52→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13273 0 198 388 13859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02213949
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.99219042
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84651729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62223.776678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.563152066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.84115107
X-RAY DIFFRACTIONr_chiral_restr0.110.21992
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111075
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6811.58609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.268213789
X-RAY DIFFRACTIONr_scbond_it1.83135340
X-RAY DIFFRACTIONr_scangle_it2.9634.55247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1407TIGHT POSITIONAL0.050.05
1A1302MEDIUM POSITIONAL0.080.5
1A1407TIGHT THERMAL0.130.5
1A1302MEDIUM THERMAL0.162
2C493TIGHT POSITIONAL0.050.05
2C443MEDIUM POSITIONAL0.050.5
2C493TIGHT THERMAL0.140.5
2C443MEDIUM THERMAL0.172
3D1502TIGHT POSITIONAL0.160.05
3D1416MEDIUM POSITIONAL0.390.5
3D1502TIGHT THERMAL0.90.5
3D1416MEDIUM THERMAL1.072
LS refinement shellResolution: 2.521→2.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 218 -
Rwork0.262 3895 -
obs--91.5 %
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)
10.081-0.15590.04980.4663-0.2420.77850.072-0.016-0.0487-0.21510.15920.11340.2149-0.1709-0.23120.1347-0.0667-0.04550.17480.04350.17444.21333.161-23.5261
20.74660.3669-0.39580.3754-0.19361.24880.04980.0095-0.07860.14170.0087-0.13430.0783-0.0476-0.05850.23010.0810.00620.1735-0.0670.198421.410534.0757-73.6277
30.42980.3066-0.36321.1193-1.23971.4030.078-0.1058-0.01510.1484-0.1270.0083-0.14290.10060.0490.13720.0030.06950.1543-0.07170.114324.26427.349225.3491
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 - 360
8X-RAY DIFFRACTION3B401 - 403

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