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- PDB-6znt: MaeB PTA domain, acetyl-CoA bound form -

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Basic information

Entry
Database: PDB / ID: 6znt
TitleMaeB PTA domain, acetyl-CoA bound form
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, 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 / DI(HYDROXYETHYL)ETHER / Malate dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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_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_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 / _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
C: Malate dehydrogenase
F: Malate dehydrogenase
D: Malate dehydrogenase
B: Malate dehydrogenase
E: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,89619
Polymers237,3396
Non-polymers5,55613
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27640 Å2
ΔGint-44 kcal/mol
Surface area73430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.190, 60.590, 167.750
Angle α, β, γ (deg.)90.000, 91.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 441 through 776)
31chain C
41chain D
51(chain E and resid 441 through 776)
61(chain F 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
2(chain B and resid 441 through 776)BE
3chain CCB
4chain DDD
5(chain E and resid 441 through 776)EF
6(chain F and resid 441 through 776)FC

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Components

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


Mass: 39556.555 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: mdh, Bd1833 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6MM15, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1M Tris pH 8.5 0.2M TMAO 20% PEG 2000 MME

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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: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.96→91.861 Å / Num. obs: 160802 / % possible obs: 99.9 % / Redundancy: 6.74 % / CC1/2: 0.99 / Net I/σ(I): 15.7
Reflection shellResolution: 1.96→2.01 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 7925 / CC1/2: 0.64

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Processing

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

1td9


Resolution: 1.96→91.861 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 7904 4.92 %RANDOM
Rwork0.1764 152807 --
obs0.1781 160711 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.73 Å2 / Biso mean: 58.0437 Å2 / Biso min: 24.1 Å2
Refinement stepCycle: final / Resolution: 1.96→91.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15537 0 352 696 16585
Biso mean--62.33 52.68 -
Num. residues----2021
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6126X-RAY DIFFRACTION4.919TORSIONAL
12B6126X-RAY DIFFRACTION4.919TORSIONAL
13C6126X-RAY DIFFRACTION4.919TORSIONAL
14D6126X-RAY DIFFRACTION4.919TORSIONAL
15E6126X-RAY DIFFRACTION4.919TORSIONAL
16F6126X-RAY DIFFRACTION4.919TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.96-1.98230.40062760.32845023100
1.9823-2.00560.32242890.29415027100
2.0056-2.03010.32952680.28865064100
2.0301-2.05580.32342790.27124981100
2.0558-2.08280.28062390.25845114100
2.0828-2.11130.26952540.2475065100
2.1113-2.14150.28742410.24065055100
2.1415-2.17350.29592730.23395105100
2.1735-2.20740.28792530.22225011100
2.2074-2.24360.25523070.21615077100
2.2436-2.28230.2622980.20835004100
2.2823-2.32380.24632740.19785100100
2.3238-2.36850.25362430.1955029100
2.3685-2.41690.22952580.19585131100
2.4169-2.46940.24422720.19385042100
2.4694-2.52690.22352930.18645096100
2.5269-2.59010.2422850.1865037100
2.5901-2.66010.26582570.18775083100
2.6601-2.73840.24862360.19125113100
2.7384-2.82680.25792850.19315057100
2.8268-2.92780.23872500.19485124100
2.9278-3.04510.24652180.19845151100
3.0451-3.18370.25762460.21295124100
3.1837-3.35150.23392680.19325079100
3.3515-3.56150.20712770.18215117100
3.5615-3.83650.20732510.17045149100
3.8365-4.22260.17332170.1485174100
4.2226-4.83360.13472480.12635178100
4.8336-6.08960.16422780.15225180100
6.0896-91.8610.16422710.1401531799
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)
12.5849-0.3698-0.41441.31840.13761.85840.0153-0.40080.45620.01290.1758-0.2405-0.17170.3471-0.13860.3143-0.0235-0.02140.4844-0.09650.4224176.4232-111.534850.6586
20.63490.0635-0.09881.21190.31132.33440.092-0.210.5141-0.0343-0.2730.3007-0.381-0.83070.16920.48480.1150.01850.8513-0.45250.9584104.884-91.598954.888
31.8774-0.2290.11221.13350.07511.0235-0.0017-0.35130.57890.0755-0.05120.0294-0.24680.0070.04090.4454-0.07090.03550.5785-0.27760.6471133.6997-96.511264.5409
41.264-0.01130.05650.68930.05741.3007-0.06-0.48140.85950.1617-0.1111-0.227-0.4645-0.23580.04130.52830.05020.00540.7226-0.44160.9808113.9266-88.759160.3538
52.7420.32770.07771.54110.41911.611-0.00840.57790.1278-0.3878-0.11620.157-0.1414-0.24140.12120.48920.0986-0.03210.39760.02140.2904139.9899-119.9217-2.3915
61.8807-0.3088-1.05141.97050.50461.84130.15570.20920.5731-0.1402-0.14390.2576-0.3283-0.40310.04280.39660.1309-0.04240.4892-0.06860.5855119.9523-106.001516.3323
72.3975-0.17280.46211.85980.56312.57630.00830.55240.7031-0.3663-0.13350.2404-0.4524-0.33680.04620.47960.1463-0.04860.51390.05570.4384132.4388-112.4937-0.2269
82.1145-0.239-0.39651.0813-0.10982.30910.10430.08610.0696-0.0395-0.14390.247-0.0012-0.53670.02210.3407-0.0272-0.00330.7512-0.30990.643493.6034-114.851238.6033
92.1461-0.2579-1.02051.94120.33561.06950.01420.1782-0.1843-0.0816-0.2080.25320.1642-0.36540.17120.3327-0.0141-0.03090.5344-0.1940.4392114.7606-128.695821.24
102.1985-0.56620.18081.27750.67561.78020.06010.287-0.23360.1177-0.23290.40710.3048-0.54920.15420.4099-0.0387-0.00120.7685-0.30840.634996.7454-122.26331.5878
110.7785-0.6289-0.44661.71290.8361.998-0.1154-1.0209-0.02340.47410.1448-0.04660.33120.6035-0.07120.548-0.0391-0.00711.23720.00630.3641152.8566-122.002180.5492
122.19360.21840.43331.3244-0.2411.29070.0402-0.5261-0.03840.1732-0.17280.22090.075-0.22660.1210.4093-0.11180.06430.7219-0.17280.4599124.4102-117.757969.669
131.70990.1572-0.13460.65990.15511.87170.0173-0.8249-0.2180.3757-0.21030.07760.24870.03720.15850.4997-0.09650.07760.9913-0.00560.4045142.0752-122.721481.3349
142.5004-0.38110.17691.48770.13941.26920.04730.354-0.3068-0.1697-0.15130.01410.1792-0.01180.08810.460.03580.02830.2288-0.0450.3435155.1619-142.825111.0617
151.36040.0452-0.020.95820.33962.23950.0314-0.2722-0.35030.0761-0.0557-0.07670.36270.06750.01780.42140.0122-0.00710.24340.10410.3802160.9138-137.817740.5732
161.3251-0.4173-0.38761.06830.09761.1309-0.06720.0422-0.2762-0.0812-0.0167-0.00430.3406-0.10370.08250.53940.02030.04750.2324-0.00240.4401159.2013-145.676820.3981
172.363-0.213-0.61281.21120.72411.57940.0586-0.98870.32370.22330.1308-0.27830.11170.4204-0.13650.3629-0.0308-0.0550.7949-0.1240.4602174.578-112.083160.9937
181.81960.1330.19761.08650.04412.33950.0264-0.00350.1251-0.13160.0086-0.0933-0.03610.119-0.03340.30490.00230.02440.17480.01930.317166.9659-116.604731.8244
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 440 through 595 )B440 - 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 'F' and (resid 439 through 595 )F439 - 595
15X-RAY DIFFRACTION15chain 'F' and (resid 596 through 736 )F596 - 736
16X-RAY DIFFRACTION16chain 'F' and (resid 737 through 776 )F737 - 776
17X-RAY DIFFRACTION17chain 'E' and (resid 439 through 595 )E439 - 595
18X-RAY DIFFRACTION18chain 'E' and (resid 596 through 736 )E596 - 736

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