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- PDB-4aah: METHANOL DEHYDROGENASE FROM METHYLOPHILUS W3A1 -

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Basic information

Entry
Database: PDB / ID: 4aah
TitleMETHANOL DEHYDROGENASE FROM METHYLOPHILUS W3A1
Components(METHANOL DEHYDROGENASE) x 2
KeywordsOXIDOREDUCTASE (PQQ(A)-CHOH(D))
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 / calcium ion binding / plasma membrane
Similarity search - Function
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 / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain ...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 / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / 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 1 / Methanol dehydrogenase [cytochrome c] subunit 2
Similarity search - Component
Biological speciesMethylophilus methylotrophus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMathews, F.S. / Xia, Z.-X.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1.
Authors: Xia, Z. / Dai, W. / Zhang, Y. / White, S.A. / Boyd, G.D. / Mathews, F.S.
#1: Journal: Biochemistry / Year: 1993
Title: The Active Site Structure of the Calcium-Containing Quinoprotein Methanol Dehydrogenase
Authors: White, S. / Boyd, G. / Mathews, F.S. / Xia, Z.X. / Dai, W.W. / Zhang, Y.F. / Davidson, V.L.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: The Three-Dimensional Structures of Methanol Dehydrogenase from Two Methylotrophic Bacteria at 2.6-A Resolution
Authors: Xia, Z.X. / Dai, W.W. / Xiong, J.P. / Hao, Z.P. / Davidson, V.L. / White, S. / Mathews, F.S.
History
DepositionMar 10, 1996Processing site: BNL
SupersessionDec 7, 1996ID: 3AAH
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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.process_site / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHANOL DEHYDROGENASE
B: METHANOL DEHYDROGENASE
C: METHANOL DEHYDROGENASE
D: METHANOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2838
Polymers140,5424
Non-polymers7414
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-85 kcal/mol
Surface area40560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.900, 62.700, 85.000
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.995206, -0.096998, 0.012534), (-0.09504, 0.989356, 0.11019), (-0.023089, 0.108471, -0.993832)
Vector: -61.54386, -2.87807, -1.53508)
DetailsMETHANOL DEHYDROGENASE IS AN A2B2 TETRAMER. THE ASYMMETRIC UNIT CONTAINS THE TETRAMER, TWO PYRROLOQUINOLINE QUINONE COFACTORS (PQQ) AND 2 CALCIUM COUNTER IONS. A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATES THE TWO HALVES.

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Components

#1: Protein METHANOL DEHYDROGENASE / MEDH


Mass: 62500.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38539, EC: 1.1.99.8
#2: Protein METHANOL DEHYDROGENASE / MEDH


Mass: 7770.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38540, EC: 1.1.99.8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AMINO ACID SEQUENCE OF MEDH FROM W3A1 WAS DERIVED FROM THE GENE SEQUENCES OF THE HEAVY AND ...THE AMINO ACID SEQUENCE OF MEDH FROM W3A1 WAS DERIVED FROM THE GENE SEQUENCES OF THE HEAVY AND LIGHT SUBUNITS IN THE LAB OF F.S. MATHEWS, GENBANK ACCESSION NUMBERS U41040 AND U41041, RESPECTIVELY. 571 RESIDUES WERE LOCATED FOR THE *A* AND *C* CHAINS AND 69 RESIDUES FOR THE *B* AND *D* CHAINS. THESE RESIDUES REPRESENT THE COMPLETE MATURE POLYPEPTIDE CHAINS FOR EACH SUBUNIT. THE GENE SEQUENCES CONTAIN A NUMBER OF ADDITIONAL BASE PAIRS ENCODING PORTIONS OF THE PERIPLASMIC SIGNAL SEQUENCES PRECEDING MATURE POLYPEPTIDE AS WELL AS FOLLOWING THE STOP CODON.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal grow
*PLUS
pH: 6.8 / Method: macro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlmethanol dehydrogenase1drop
25 mMphosphate1drop
310 mMmethanol1drop
450 mMTris-HCl1reservoir
512.0 %(w/v)PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 51578 / % possible obs: 99.5 % / Observed criterion σ(I): 0
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.59 Å / Mean I/σ(I) obs: 3.4

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.4→10 Å / σ(F): 1
Details: THE STRUCTURE WAS SOLVED BY MULTIPLE ISOMORPHOUS REPLACEMENT USING THREE DERIVATIVES. THE STRUCTURE WAS SOLVED BY MULTIPLE ISOMORPHOUS REPLACEMENT USING THREE DERIVATIVES.
RfactorNum. reflection% reflection
obs0.152 50837 99.5 %
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9894 0 50 521 10465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0340.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.641
X-RAY DIFFRACTIONp_mcangle_it1.081.5
X-RAY DIFFRACTIONp_scbond_it1.261.5
X-RAY DIFFRACTIONp_scangle_it1.952
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1650.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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