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- PDB-6zne: MaeB PTA domain R535E mutant -

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Basic information

Entry
Database: PDB / ID: 6zne
TitleMaeB PTA domain R535E mutant
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 / 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, 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: 2.393 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 / 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 / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _chem_comp.formula ..._atom_site.label_seq_id / _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_unobs_or_zero_occ_atoms.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.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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
D: Malate dehydrogenase
F: Malate dehydrogenase
E: Malate dehydrogenase
C: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)237,1716
Polymers237,1716
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15030 Å2
ΔGint-68 kcal/mol
Surface area77570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.420, 183.400, 120.237
Angle α, β, γ (deg.)90.000, 117.030, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERchain AAA439 - 77621 - 358
2SERSERchain BBB439 - 77621 - 358
3ARGARGchain CCF439 - 77721 - 359
4SERSERchain DDC439 - 77621 - 358
5SERSERchain EEE439 - 77621 - 358
6SERSERchain FFD439 - 77621 - 358

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Components

#1: Protein
Malate dehydrogenase


Mass: 39528.477 Da / Num. of mol.: 6 / Mutation: R535E
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 / Variant: R535E / Production host: Escherichia coli (E. coli)
References: UniProt: Q6MM15, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Hepes pH 7.5 0.1M Magnesium Chloride 10% PEG 400 15% PEG smear medium 5% propan-2-ol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.39→97.603 Å / Num. obs: 96539 / % possible obs: 98.4 % / Redundancy: 4.6 % / CC1/2: 0.99 / Net I/σ(I): 8.5
Reflection shellResolution: 2.39→2.5 Å / Num. unique obs: 4863 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TD9

1td9


Resolution: 2.393→69.657 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 4762 4.94 %
Rwork0.2153 91608 -
obs0.2175 96370 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.41 Å2 / Biso mean: 75.4813 Å2 / Biso min: 44.6 Å2
Refinement stepCycle: final / Resolution: 2.393→69.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15581 0 0 47 15628
Biso mean---65.66 -
Num. residues----2029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115845
X-RAY DIFFRACTIONf_angle_d1.41521451
X-RAY DIFFRACTIONf_chiral_restr0.0562497
X-RAY DIFFRACTIONf_plane_restr0.0082785
X-RAY DIFFRACTIONf_dihedral_angle_d13.4285977
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9652X-RAY DIFFRACTION11.413TORSIONAL
12B9652X-RAY DIFFRACTION11.413TORSIONAL
13C9652X-RAY DIFFRACTION11.413TORSIONAL
14D9652X-RAY DIFFRACTION11.413TORSIONAL
15E9652X-RAY DIFFRACTION11.413TORSIONAL
16F9652X-RAY DIFFRACTION11.413TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.393-2.42020.45761500.4151304298
2.4202-2.44870.371530.4127308899
2.4487-2.47850.43731450.4014307399
2.4785-2.50990.38161630.38723091100
2.5099-2.54290.38661590.3672306899
2.5429-2.57780.39611580.37413099100
2.5778-2.61460.41271920.35993088100
2.6146-2.65360.40221580.34763049100
2.6536-2.69510.39051750.33273097100
2.6951-2.73930.35781660.32893093100
2.7393-2.78650.36141410.31363119100
2.7865-2.83720.34151570.30933097100
2.8372-2.89180.30931620.31023097100
2.8918-2.95080.33711890.3033107100
2.9508-3.0150.32341590.30013074100
3.015-3.08510.38661590.28013115100
3.0851-3.16220.37331510.25793109100
3.1622-3.24770.26141820.24333076100
3.2477-3.34330.30141510.2313098100
3.3433-3.45120.27511020.2386224897
3.4512-3.57460.2841420.2324262299
3.5746-3.71770.25281420.21823131100
3.7177-3.88690.25921560.20663106100
3.8869-4.09180.22461540.18593114100
4.0918-4.34810.22851640.16793106100
4.3481-4.68370.19371790.14823096100
4.6837-5.1550.20211530.15443101100
5.155-5.90060.23181740.18133139100
5.9006-7.43270.1941630.16613122100
7.4327-69.6570.17321630.1291314399

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