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- PDB-1h4j: Methylobacterium extorquens methanol dehydrogenase D303E mutant -

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Basic information

Entry
Database: PDB / ID: 1h4j
TitleMethylobacterium extorquens methanol dehydrogenase D303E mutant
Components
  • Methanol dehydrogenase [cytochrome c] subunit 1
  • Methanol dehydrogenase [cytochrome c] subunit 2
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / QUINOPROTEIN
Function / homology
Function and homology information


methanol dehydrogenase (cytochrome c) / methanol oxidation / alcohol dehydrogenase (cytochrome c(L)) activity / methanol metabolic process / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding / plasma membrane
Similarity search - Function
Bacterial quinoprotein dehydrogenases signature 1. / Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family ...Bacterial quinoprotein dehydrogenases signature 1. / Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / PQQ enzyme repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Methanol dehydrogenase [cytochrome c] subunit 2 / Methanol dehydrogenase [cytochrome c] subunit 1
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMohammed, F. / Gill, R. / Thompson, D. / Cooper, J.B. / Wood, S.P. / Afolabi, P.R. / Anthony, C.
CitationJournal: Biochemistry / Year: 2001
Title: Site-Directed Mutagenesis and X-Ray Crystallography of the Pqq-Containing Quinoprotein Methanol Dehydrogenase and its Electron Acceptor, Cytochrome C(L)(,)
Authors: Afolabi, P.R. / Mohammed, F. / Amaratunga, K. / Majekodunmi, O. / Dales, S.L. / Gill, R. / Thompson, D. / Cooper, J.B. / Wood, S.P. / Goodwin, P.M. / Anthony, C.
History
DepositionMay 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _entity.pdbx_description ..._citation.page_last / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id
Revision 1.4May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.pdbx_dist_value / _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_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_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

Downloads & links

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Assembly

Deposited unit
A: Methanol dehydrogenase [cytochrome c] subunit 1
B: Methanol dehydrogenase [cytochrome c] subunit 2
C: Methanol dehydrogenase [cytochrome c] subunit 1
D: Methanol dehydrogenase [cytochrome c] subunit 2
E: Methanol dehydrogenase [cytochrome c] subunit 1
F: Methanol dehydrogenase [cytochrome c] subunit 2
G: Methanol dehydrogenase [cytochrome c] subunit 1
H: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,92716
Polymers297,4468
Non-polymers1,4818
Water00
1
A: Methanol dehydrogenase [cytochrome c] subunit 1
B: Methanol dehydrogenase [cytochrome c] subunit 2
C: Methanol dehydrogenase [cytochrome c] subunit 1
D: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,4648
Polymers148,7234
Non-polymers7414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13180 Å2
ΔGint-69.2 kcal/mol
Surface area50850 Å2
MethodPQS
2
E: Methanol dehydrogenase [cytochrome c] subunit 1
F: Methanol dehydrogenase [cytochrome c] subunit 2
G: Methanol dehydrogenase [cytochrome c] subunit 1
H: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,4648
Polymers148,7234
Non-polymers7414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-71.5 kcal/mol
Surface area50830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.850, 61.020, 212.680
Angle α, β, γ (deg.)90.00, 92.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methanol dehydrogenase [cytochrome c] subunit 1 / MDH large subunit alpha / MEDH


Mass: 65880.859 Da / Num. of mol.: 4 / Mutation: D303E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: moxF, mxaF, MexAM1_META1p4538 / Production host: Escherichia coli (E. coli)
References: UniProt: P16027, methanol dehydrogenase (cytochrome c)
#2: Protein
Methanol dehydrogenase [cytochrome c] subunit 2 / MDH small subunit beta / MDH-associated peptide / MEDH


Mass: 8480.620 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PYRROLO-QUINOLINE QUINONE PROSTHETIC GROUP WITH ACTIVE SITE CALCIUM IONS
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: moxI, mxaI, MexAM1_META1p4535 / Production host: Escherichia coli (E. coli)
References: UniProt: P14775, methanol dehydrogenase (cytochrome c)
#3: Chemical
ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Compound detailsCHAIN A, C, E, G ENGINEERED MUTATION ASP303GLU

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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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growpH: 9.5 / Details: pH 9.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114.5 %PEG60001reservoir
220 mMTris-HCl1reservoir
310 mM1reservoirCaCl2
420 mg/mlprotein1drop
55 mMTris1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 48502 / % possible obs: 91.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.9
Reflection shellResolution: 3→3.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.6 / % possible all: 81.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 134792
Reflection shell
*PLUS
% possible obs: 81.4 %

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Processing

Software
NameClassification
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE STRUCTURE

Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2385 5 %RANDOM
Rwork0.187 ---
obs0.187 45246 91.5 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20808 0 100 0 20908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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