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- PDB-2gc4: Structural comparison of the oxidized ternary electron transfer c... -

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Basic information

Entry
Database: PDB / ID: 2gc4
TitleStructural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.
Components
  • (Methylamine dehydrogenase ...Amine dehydrogenase) x 2
  • Amicyanin
  • Cytochrome c-L
KeywordsOxidoreductase / Electron transport / Electron transfer / Methylamine dehydrogenase / Cytochrome / Blue copper protein
Function / homology
Function and homology information


methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / electron transfer activity / periplasmic space / iron ion binding ...methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / electron transfer activity / periplasmic space / iron ion binding / copper ion binding / heme binding
Similarity search - Function
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 ...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 / 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 / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Cytochrome c-L
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, Z. / Durley, R. / Davidson, V.L. / Mathews, F.S.
Citation
Journal: To be Published
Title: Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, ...Title: Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.
Authors: Chen, Z. / Durley, R. / Davidson, V.L. / Mathews, F.S.
#1: Journal: Science / Year: 1994
Title: Structure of an electron transfer complex: methylamine dehydrogenase, amicyanin and cytochrome c551i.
Authors: Chen, L. / Durley, R. / Mathews, F.S. / Davidson, V.L.
History
DepositionMar 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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 2.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)340,58028
Polymers337,76016
Non-polymers2,82012
Water20,5371140
1
A: Methylamine dehydrogenase heavy chain
B: Methylamine dehydrogenase light chain
C: Amicyanin
D: Cytochrome c-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1457
Polymers84,4404
Non-polymers7053
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)85,1457
Polymers84,4404
Non-polymers7053
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Methylamine dehydrogenase heavy chain
J: Methylamine dehydrogenase light chain
K: Amicyanin
L: Cytochrome c-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1457
Polymers84,4404
Non-polymers7053
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
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)85,1457
Polymers84,4404
Non-polymers7053
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.368, 188.979, 128.836
Angle α, β, γ (deg.)90.00, 99.74, 90.00
Int Tables number4
Space group name H-MP1211

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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 natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P22364
#4: Protein
Cytochrome c-L / Cytochrome c551I / Cytochrome c552


Mass: 16274.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P29899

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

#1: Protein
Methylamine dehydrogenase heavy chain / Amine dehydrogenase / MADH


Mass: 42449.277 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P29894, EC: 1.4.99.3
#2: Antibody
Methylamine dehydrogenase light chain / Amine dehydrogenase / MADH


Mass: 14210.696 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P22619, EC: 1.4.99.3

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Non-polymers , 4 types, 1152 molecules

#5: Chemical
ChemComp-CU / COPPER (II) ION / Copper


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


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


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


Mass: 18.015 Da / Num. of mol.: 1140 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.3-2.6M Sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.95 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 25, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 303065 / Num. obs: 254878 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.1 / Num. unique all: 13067 / % possible all: 43.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MTA

2mta


Resolution: 1.9→29.95 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 229046.41 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 20266 8 %RANDOM
Rwork0.173 ---
all-300340 --
obs-253468 84.3 %-
Displacement parametersBiso mean: 34.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23500 0 180 1140 24820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
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 RworkNum. reflection obs
1.9-2.020.311319327.90.29122253422302
2.02-2.170.25332170.232237099
2.17-2.390.23437140.196841960
2.39-2.740.224437420.191242844
2.74-3.450.207738160.179444283
3.45-29.950.156238457.90.13952253444714

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