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- PDB-6zn9: MaeB PTA domain apoprotein -

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Basic information

Entry
Database: PDB / ID: 6zn9
TitleMaeB PTA domain apoprotein
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malic enzyme
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / acyltransferase activity / NAD 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, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain ...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, 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
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 / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _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_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_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_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jan 31, 2024Group: 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
C: Malate dehydrogenase
D: Malate dehydrogenase
A: Malate dehydrogenase
B: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
J: Malate dehydrogenase
L: Malate dehydrogenase
H: Malate dehydrogenase
I: Malate dehydrogenase
K: Malate dehydrogenase
E: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)474,67912
Polymers474,67912
Non-polymers00
Water0
1
C: Malate dehydrogenase
D: Malate dehydrogenase
J: Malate dehydrogenase
L: Malate dehydrogenase
I: Malate dehydrogenase
K: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)237,3396
Polymers237,3396
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Malate dehydrogenase
B: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
E: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)237,3396
Polymers237,3396
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.215, 151.278, 285.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Malate dehydrogenase /


Mass: 39556.555 Da / Num. of mol.: 12
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: mdh, Bd1833 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6MM15, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)

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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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M Sodium Acetate pH 4.5 0.1M Magnesium Acetate 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.72→142.66 Å / Num. obs: 162146 / % possible obs: 99.9 % / Redundancy: 12.84 % / CC1/2: 0.99 / Net I/σ(I): 11.4
Reflection shellResolution: 2.72→2.76 Å / Num. unique obs: 7836 / CC1/2: 0.6

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Processing

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

1td9


Resolution: 2.72→99.637 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.299 --
Rwork0.252 --
obs-154701 100 %
Displacement parametersBiso max: 274.3 Å2 / Biso mean: 85.7841 Å2 / Biso min: 30.67 Å2
Refinement stepCycle: LAST / Resolution: 2.72→99.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31268 0 0 0 31268

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