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- PDB-6zng: MaeB full-length acetyl-CoA bound state -

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Basic information

Entry
Database: PDB / ID: 6zng
TitleMaeB full-length acetyl-CoA bound state
ComponentsNADP-dependent malate dehydrogenase,Malate dehydrogenase
KeywordsOXIDOREDUCTASE / malic enzyme
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / acyltransferase activity / NAD binding / metal ion binding
Similarity search - Function
Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily ...Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / NADP-dependent malate dehydrogenase / Malate dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsLovering, A.L. / Harding, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)mibtp studentship United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: A rotary mechanism for allostery in bacterial hybrid malic enzymes.
Authors: Harding, C.J. / Cadby, I.T. / Moynihan, P.J. / Lovering, A.L.
History
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent malate dehydrogenase,Malate dehydrogenase
B: NADP-dependent malate dehydrogenase,Malate dehydrogenase
C: NADP-dependent malate dehydrogenase,Malate dehydrogenase
D: NADP-dependent malate dehydrogenase,Malate dehydrogenase
E: NADP-dependent malate dehydrogenase,Malate dehydrogenase
F: NADP-dependent malate dehydrogenase,Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,58612
Polymers515,7286
Non-polymers4,8576
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51470 Å2
ΔGint-281 kcal/mol
Surface area160480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.422, 144.792, 171.138
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NADP-dependent malate dehydrogenase,Malate dehydrogenase


Mass: 85954.711 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd1834, mdh, Bd1833 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6MM14, UniProt: Q6MM15, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
Has ligand of interestN

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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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Bistris Propane pH 8.5 0.2M sodium citrate tribasic monohydrate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.72→124.801 Å / Num. obs: 160818 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 11
Reflection shellResolution: 2.72→2.86 Å / Num. unique obs: 8003 / CC1/2: 0.32

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXv1.0refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CEE, 1TD9

5cee

1td9


Resolution: 2.72→109.382 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.23 --
Rwork0.19 --
obs-159743 99.2 %
Displacement parametersBiso max: 311.17 Å2 / Biso mean: 108.0413 Å2 / Biso min: 46.39 Å2
Refinement stepCycle: LAST / Resolution: 2.72→109.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34291 0 306 0 34597

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