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- PDB-6znu: MaeB PTA domain E544R mutant -

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Basic information

Entry
Database: PDB / ID: 6znu
TitleMaeB PTA domain E544R mutant
ComponentsMalate 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, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal 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
ACETYL COENZYME *A / Malate dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / citation_author / entity / entity_name_com / 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 / 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 / _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.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _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_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.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
G: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,57818
Polymers237,5086
Non-polymers5,07012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24040 Å2
ΔGint-135 kcal/mol
Surface area74380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.090, 182.850, 119.660
Angle α, β, γ (deg.)90.000, 117.690, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and resid 441 through 776)
41(chain D and resid 441 through 776)
51(chain E and resid 441 through 776)
61(chain G and resid 441 through 776)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 441 - 776 / Label seq-ID: 23 - 358

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBC
3(chain C and resid 441 through 776)CD
4(chain D and resid 441 through 776)DE
5(chain E and resid 441 through 776)EF
6(chain G and resid 441 through 776)GB

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Components

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


Mass: 39584.637 Da / Num. of mol.: 6 / Mutation: E544R
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: E544R mutant / Production host: Escherichia coli (E. coli)
References: 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Hepes pH 7.5 0.2M Magnesium Chloride 10% ethylene glycol 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 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.33→69.22 Å / Num. obs: 104231 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 12.03
Reflection shellResolution: 2.33→2.5 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 5084 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TD9

1td9


Resolution: 2.33→56.863 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 5234 5.02 %
Rwork0.1961 98981 -
obs0.1981 104215 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.37 Å2 / Biso mean: 62.0267 Å2 / Biso min: 25.8 Å2
Refinement stepCycle: final / Resolution: 2.33→56.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15547 0 312 0 15859
Biso mean--93.17 --
Num. residues----2021
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6132X-RAY DIFFRACTION6.279TORSIONAL
12B6132X-RAY DIFFRACTION6.279TORSIONAL
13C6132X-RAY DIFFRACTION6.279TORSIONAL
14D6132X-RAY DIFFRACTION6.279TORSIONAL
15E6132X-RAY DIFFRACTION6.279TORSIONAL
16G6132X-RAY DIFFRACTION6.279TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.33-2.35650.41271630.3742319997
2.3565-2.38420.34751680.34413301100
2.3842-2.41330.41471630.3253263100
2.4133-2.44380.3631680.3033305100
2.4438-2.4760.3251530.28873312100
2.476-2.50990.3191750.27213275100
2.5099-2.54580.32031590.26433357100
2.5458-2.58380.30831770.2543268100
2.5838-2.62420.33031910.25053264100
2.6242-2.66720.30731750.24613326100
2.6672-2.71320.28231560.24283314100
2.7132-2.76250.26931680.2423289100
2.7625-2.81560.27221810.23743309100
2.8156-2.87310.31011990.24823291100
2.8731-2.93560.28271890.24743258100
2.9356-3.00390.27831660.24263276100
3.0039-3.0790.2871990.23543298100
3.079-3.16220.28161550.2313291100
3.1622-3.25530.2771340.23363347100
3.2553-3.36030.27311760.22323295100
3.3603-3.48040.24921780.22283313100
3.4804-3.61970.23751950.20893295100
3.6197-3.78440.23031640.18883306100
3.7844-3.98390.1971740.17073313100
3.9839-4.23340.22581760.15693295100
4.2334-4.56020.18651990.14533302100
4.5602-5.01880.17751950.14173311100
5.0188-5.74450.22841770.17553320100
5.7445-7.23510.21961760.17823324100
7.2351-56.8630.16121850.141336499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19440.2103-0.8228-0.0253-0.24050.641-0.318-0.1325-1.14050.18440.06920.13390.0645-0.2132-0.02830.54120.09740.0510.53120.07710.5728-30.1497-28.000635.8036
21.276-0.6495-0.52843.64290.27271.5497-0.18730.0022-0.38010.13740.07120.12660.2027-0.0213-0.00040.3893-0.0364-0.01140.3295-0.03090.4673-72.739-26.155132.2693
31.5284-0.66630.09261.99930.48371.0245-0.0168-0.08130.055-0.0292-0.00220.3048-0.0782-0.1229-0.00030.3550.0077-0.05950.4035-0.0150.2752-78.13173.760535.9646
40.5519-0.3106-0.36540.92390.25790.2847-0.2518-0.0985-0.03760.1283-0.04070.82550.0919-0.2936-0.0010.5068-0.0184-0.09790.4977-0.06830.5207-79.2456-17.348732.6793
51.9521-0.6528-0.98451.7940.30681.30940.10960.11380.1583-0.02870.00460.0891-0.1713-0.1780.00040.33570.084-0.03150.30880.02030.398-70.181346.33830.3225
61.6698-0.183-0.69910.35010.31841.20640.12080.29670.0069-0.2474-0.1202-0.2484-0.2532-0.1234-0.00020.51120.05940.03670.4568-0.02570.4984-46.345336.78313.6033
70.6456-0.1978-0.51420.27190.02190.48030.25240.32510.0617-0.0909-0.116-0.1735-0.3522-0.1546-0.00080.53020.11430.00930.517-0.01830.4661-63.709746.502621.6318
81.7343-0.9428-0.79381.9326-0.67830.52540.2849-0.30540.45870.4733-0.01470.2735-0.40960.15830.0040.6252-0.09370.17610.5546-0.24520.5206-71.064629.961259.0386
90.7249-0.196-0.47621.9003-0.04831.4361-0.2231-0.3644-0.20810.28770.1351-0.06280.23160.2441-0.00010.4230.0766-0.06810.5829-0.01910.2844-63.5480.704854.3235
100.4861-0.20090.08020.8192-0.36280.1570.1539-0.34050.0980.54030.11740.316-0.2921-0.09290.12320.6959-0.0190.08750.6355-0.18560.316-69.320119.779162.1847
113.11760.6918-1.03612.3301-0.28381.46530.08540.22570.1743-0.1377-0.0273-0.1612-0.11990.03080.00010.41540.0382-0.03350.44430.03770.1489-20.63117.4412-5.4678
121.10550.645-0.82371.3956-0.35691.4112-0.20430.1937-0.25490.00390.08410.25670.2241-0.2125-00.3522-0.0177-0.05320.4246-0.03490.2996-38.9539-12.9798.1587
130.45320.5821-0.06261.31670.1610.3384-0.18270.1661-0.266-0.12970.1279-0.1004-0.001-0.02840.00130.4506-0.0154-0.06950.5206-0.00940.2658-26.6469-1.4864-5.1442
140.7434-0.724-0.59721.71840.57331.15270.14440.00980.116-0.25170.1068-0.4559-0.12520.16970.00330.4066-0.05150.11680.3812-0.07390.6989-11.237130.736417.8063
151.8519-0.5945-0.36021.36420.7481.56410.0752-0.16310.1980.0132-0.0136-0.042-0.1364-0.0453-0.00070.3722-0.015-0.00110.3773-0.02290.5829-35.760137.910434.7558
160.3572-0.5199-0.35660.74570.60830.4580.1848-0.06460.1357-0.27050.2023-0.2671-0.16990.1584-0.00040.4706-0.07470.05260.471-0.07030.8509-16.519336.352125.5943
172.41710.5032-0.9012.0369-0.11021.7966-0.2437-0.0219-0.75390.13720.0570.1670.1908-0.21370.00290.47070.09160.04880.49120.13660.55-39.8188-32.511538.6975
182.10940.40910.13621.4189-0.9441.6087-0.07250.02660.08430.0443-0.0214-0.2349-0.02680.1135-0.00020.37840.0323-0.05280.35790.01930.2689-22.9245-10.525525.4547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 737 through 776 )E737 - 776
2X-RAY DIFFRACTION2chain 'C' and (resid 441 through 595 )C441 - 595
3X-RAY DIFFRACTION3chain 'C' and (resid 596 through 736 )C596 - 736
4X-RAY DIFFRACTION4chain 'C' and (resid 737 through 776 )C737 - 776
5X-RAY DIFFRACTION5chain 'A' and (resid 441 through 595 )A441 - 595
6X-RAY DIFFRACTION6chain 'A' and (resid 596 through 736 )A596 - 736
7X-RAY DIFFRACTION7chain 'A' and (resid 737 through 776 )A737 - 776
8X-RAY DIFFRACTION8chain 'B' and (resid 441 through 595 )B441 - 595
9X-RAY DIFFRACTION9chain 'B' and (resid 596 through 736 )B596 - 736
10X-RAY DIFFRACTION10chain 'B' and (resid 737 through 776 )B737 - 776
11X-RAY DIFFRACTION11chain 'D' and (resid 441 through 595 )D441 - 595
12X-RAY DIFFRACTION12chain 'D' and (resid 596 through 736 )D596 - 736
13X-RAY DIFFRACTION13chain 'D' and (resid 737 through 776 )D737 - 776
14X-RAY DIFFRACTION14chain 'G' and (resid 441 through 595 )G441 - 595
15X-RAY DIFFRACTION15chain 'G' and (resid 596 through 736 )G596 - 736
16X-RAY DIFFRACTION16chain 'G' and (resid 737 through 776 )G737 - 776
17X-RAY DIFFRACTION17chain 'E' and (resid 441 through 595 )E441 - 595
18X-RAY DIFFRACTION18chain 'E' and (resid 596 through 736 )E596 - 736

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