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- PDB-6znj: MaeB full-length enzyme apoprotein form -

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Basic information

Entry
Database: PDB / ID: 6znj
TitleMaeB full-length enzyme apoprotein form
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
Rossmann fold - #10950 / 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 ...Rossmann fold - #10950 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP-dependent malate dehydrogenase / Malate dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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_seq / struct_ref_seq_dif / struct_sheet_range
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_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _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_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

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Assembly

Deposited unit
B: NADP-dependent malate dehydrogenase,Malate dehydrogenase
C: NADP-dependent malate dehydrogenase,Malate dehydrogenase
A: NADP-dependent malate dehydrogenase,Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)257,8643
Polymers257,8643
Non-polymers00
Water00
1
B: NADP-dependent malate dehydrogenase,Malate dehydrogenase
C: NADP-dependent malate dehydrogenase,Malate dehydrogenase
A: NADP-dependent malate dehydrogenase,Malate dehydrogenase

B: NADP-dependent malate dehydrogenase,Malate dehydrogenase
C: NADP-dependent malate dehydrogenase,Malate dehydrogenase
A: NADP-dependent malate dehydrogenase,Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)515,7286
Polymers515,7286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)81.705, 273.583, 308.232
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 85954.711 Da / Num. of mol.: 3
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+)

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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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: 0.1M Tris pH 8.0 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 3.7→154.12 Å / Num. obs: 36296 / % possible obs: 97.1 % / Redundancy: 13 % / CC1/2: 0.96 / Net I/σ(I): 4.6
Reflection shellResolution: 3.7→4 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1825 / CC1/2: 0.48

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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: 5CEE, 1TD9

5cee

1td9


Resolution: 3.7→66.772 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.27 --
Rwork0.21 --
obs-36052 96.49 %
Displacement parametersBiso max: 199.03 Å2 / Biso mean: 103.1654 Å2 / Biso min: 57.21 Å2
Refinement stepCycle: LAST / Resolution: 3.7→66.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17376 0 0 0 17376

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