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- PDB-1mg2: MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE R... -

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Basic information

Entry
Database: PDB / ID: 1mg2
TitleMUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN
Components
  • (Methylamine dehydrogenase, ...) x 2
  • Amicyanin
  • CYTOCHROME C-L
KeywordsOXIDOREDUCTASE / electron transfer / methylamine dehydrogenase / cytochrome / blue copper protein / active site mutant
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards cell periphery / methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / host cell / outer membrane-bounded periplasmic space / host cell endosome ...microtubule-dependent intracellular transport of viral material towards cell periphery / methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / host cell / outer membrane-bounded periplasmic space / host cell endosome / periplasmic space / electron transfer activity / iron ion binding / copper ion binding / heme binding / virion membrane / membrane
Similarity search - Function
Poxvirus F12L / Poxvirus F12L protein / Cytochrome cL / Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain ...Poxvirus F12L / Poxvirus F12L protein / Cytochrome cL / Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / 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 / Amicyanin/Pseudoazurin / Quinoprotein amine dehydrogenase, beta chain-like / Blue (type 1) copper protein, plastocyanin-type / Cytochrome C oxidase, cbb3-type, subunit III / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Ribonuclease H-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME C / PHOSPHATE ION / Amicyanin / Methylamine dehydrogenase light chain / Protein OPG056 / Methylamine dehydrogenase heavy chain / Cytochrome c-L
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSun, D. / Chen, Z.W. / Mathews, F.S. / Davidson, V.L.
Citation
Journal: Biochemistry / Year: 2002
Title: MUTATION OF AlPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN
Authors: Sun, D. / Chen, Z.W. / Mathews, F.S. / Davidson, V.L.
#1: Journal: Science / Year: 1994
Title: Structureof an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i.
Authors: Chen, L. / Durley, R. / Mathews, F.S. / Davidson, V.L.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE The authors maintain that the sequence in the sequence database is wrong.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylamine dehydrogenase, heavy chain
B: Methylamine dehydrogenase, light chain
C: Amicyanin
D: CYTOCHROME C-L
E: Methylamine dehydrogenase, heavy chain
F: Methylamine dehydrogenase, light chain
G: Amicyanin
H: CYTOCHROME C-L
I: Methylamine dehydrogenase, heavy chain
J: Methylamine dehydrogenase, light chain
K: Amicyanin
L: CYTOCHROME C-L
M: Methylamine dehydrogenase, heavy chain
N: Methylamine dehydrogenase, light chain
O: Amicyanin
P: CYTOCHROME C-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,51636
Polymers341,93616
Non-polymers3,58020
Water30,3551685
1
A: Methylamine dehydrogenase, heavy chain
B: Methylamine dehydrogenase, light chain
C: Amicyanin
D: CYTOCHROME C-L
E: Methylamine dehydrogenase, heavy chain
F: Methylamine dehydrogenase, light chain
G: Amicyanin
H: CYTOCHROME C-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,75818
Polymers170,9688
Non-polymers1,79010
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Methylamine dehydrogenase, heavy chain
J: Methylamine dehydrogenase, light chain
K: Amicyanin
L: CYTOCHROME C-L
M: Methylamine dehydrogenase, heavy chain
N: Methylamine dehydrogenase, light chain
O: Amicyanin
P: CYTOCHROME C-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,75818
Polymers170,9688
Non-polymers1,79010
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.122, 188.201, 127.100
Angle α, β, γ (deg.)90.00, 99.24, 90.00
Int Tables number4
Space group name H-MP1211
Detailstwo heterooctameric molecules per asymmetric unit

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Components

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Protein , 2 types, 8 molecules CGKODHLP

#3: Protein
Amicyanin


Mass: 11505.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22364
#4: Protein
CYTOCHROME C-L / CYTOCHROME C551I


Mass: 17094.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P29889, UniProt: P29899*PLUS

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Methylamine dehydrogenase, ... / Antibody , 2 types, 8 molecules AEIMBFJN

#1: Protein
Methylamine dehydrogenase, heavy chain / MADH


Mass: 42673.492 Da / Num. of mol.: 4 / Mutation: alpha F55A of methylamine dehydrogenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P29894, EC: 1.4.99.3
#2: Antibody
Methylamine dehydrogenase, light chain / MADH


Mass: 14210.696 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22619, EC: 1.4.99.3

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Non-polymers , 5 types, 1705 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1685 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.6 mg/mlalphaF55A MADH1drop
22.9 mg/mlamicyanin1drop
34.8 mg/mlcytochrome c-551i1drop
45 mMsodium potassium phosphate1droppH5.0
52.4 Msodium potassium monobasic/dibasic phosphate buffer1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 6, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 173239 / Num. obs: 150718 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4 / Num. unique all: 8212 / % possible all: 47.4
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / % possible obs: 47.4 %

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MTA

2mta


Resolution: 2.25→50 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 15071 10 %RANDOM
Rwork0.173 ---
all-173306 --
obs-150643 86.9 %-
Solvent computationBsol: 35.5258 Å2 / ksol: 0.384412 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23472 0 220 1685 25377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.781.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.992
X-RAY DIFFRACTIONc_scangle_it4.022.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.25-2.390.2735150910.10.2231135230.0071342352.1
2.39-2.570.264522080.216619873
2.57-2.830.236727390.187625041
2.83-3.240.220928180.178125483
3.24-4.090.189229150.157425859
4.09-500.176928820.150925893
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Lowest resolution: 2.3 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.222

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