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- PDB-6znr: MaeB PTA domain R535A mutant -

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Basic information

Entry
Database: PDB / ID: 6znr
TitleMaeB PTA domain R535A 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: 2.217 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 1.1Mar 17, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_name_com / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._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_src_gen.gene_src_strain
Revision 1.2Jan 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)236,8236
Polymers236,8236
Non-polymers00
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-67 kcal/mol
Surface area78400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.240, 183.116, 119.527
Angle α, β, γ (deg.)90.000, 117.080, 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 439 through 776)
41(chain D and (resid 437 or resid 440 through 776))
51chain E
61chain F

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERchain AAA439 - 77621 - 358
21SERSERchain BBB439 - 77621 - 358
31SERSER(chain C and resid 439 through 776)CF439 - 77621 - 358
41SERSER(chain D and (resid 437 or resid 440 through 776))DC43719
42LYSLYS(chain D and (resid 437 or resid 440 through 776))DC440 - 77622 - 358
51SERSERchain EEE439 - 77621 - 358
61SERSERchain FFD439 - 77621 - 358

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Components

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


Mass: 39470.441 Da / Num. of mol.: 6 / Mutation: R535A
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: R535A mutant / 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.: 432 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Hepes pH 7.5 0.2M Magnesium Chloride 10% ethylene glycol

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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: 2.217→69.407 Å / Num. obs: 119552 / % possible obs: 99.9 % / Redundancy: 6.81 % / CC1/2: 0.99 / Net I/σ(I): 10.69
Reflection shellResolution: 2.35→2.5 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 5235 / CC1/2: 0.57

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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: 2.217→69.407 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 6021 5.04 %
Rwork0.1887 113531 -
obs0.1908 119552 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.7 Å2 / Biso mean: 57.3806 Å2 / Biso min: 21.56 Å2
Refinement stepCycle: final / Resolution: 2.217→69.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15573 0 0 432 16005
Biso mean---50.7 -
Num. residues----2031
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6153X-RAY DIFFRACTION7.695TORSIONAL
12B6153X-RAY DIFFRACTION7.695TORSIONAL
13C6153X-RAY DIFFRACTION7.695TORSIONAL
14D6153X-RAY DIFFRACTION7.695TORSIONAL
15E6153X-RAY DIFFRACTION7.695TORSIONAL
16F6153X-RAY DIFFRACTION7.695TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.217-2.24170.41781800.4026319282
2.2417-2.26810.45621960.3782367996
2.2681-2.29570.4071920.3508373497
2.2957-2.32480.39582190.3262373397
2.3248-2.35540.39022010.3172376797
2.3554-2.38770.34321790.2976378297
2.3877-2.42180.30641780.2843375298
2.4218-2.45790.30652020.2696377498
2.4579-2.49630.30712320.2615377998
2.4963-2.53730.31021960.2554374797
2.5373-2.5810.31071820.2499375897
2.581-2.62790.2931850.2483379198
2.6279-2.67850.31382050.2477375997
2.6785-2.73320.26431960.2487379498
2.7332-2.79260.30612270.2348375698
2.7926-2.85760.30411990.2154381599
2.8576-2.9290.26762000.2162378898
2.929-3.00820.25122120.2165382499
3.0082-3.09670.2752050.2007380099
3.0967-3.19670.26372060.2382999
3.1967-3.31090.24311990.2031383399
3.3109-3.44350.24611990.1891383899
3.4435-3.60020.22992110.1761385599
3.6002-3.790.19981780.16213862100
3.79-4.02750.21211720.1597390099
4.0275-4.33840.16911920.1417386899
4.3384-4.77490.17792310.12813819100
4.7749-5.46560.17632130.14843892100
5.4656-6.88510.21442060.183892100
6.8851-69.4070.15792280.1413919100
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)
11.5956-0.2888-0.89950.9568-0.07670.43150.102-0.2565-0.0450.09850.09160.4855-0.1576-0.27520.00290.5478-0.06030.01450.3618-0.07560.4831-79.1271-17.483932.6287
22.7983-0.2965-0.44493.2710.1221.60660.1150.3482-0.0241-0.4234-0.109-0.3546-0.12140.00830.00060.31810.00390.01160.40860.02610.1053-20.42677.4887-5.8475
31.44820.2916-1.04981.6145-0.43732.405-0.2230.332-0.3604-0.06510.06160.2410.4214-0.3149-0.00040.3056-0.07260.01550.3588-0.03730.3792-39.1201-12.8017.7261
40.74440.6802-0.21591.34960.25830.377-0.06560.3958-0.2478-0.34720.0611-0.06880.1864-0.00050.00010.3776-0.0407-0.02230.46110.02140.2726-26.686-1.4056-5.4905
52.745-0.0533-1.29031.83570.19361.97410.31440.31880.5415-0.0065-0.05340.273-0.2929-0.19570.01920.30970.1302-0.03120.27780.04260.3886-70.253246.453129.9749
62.9821-0.7595-1.2621.0720.50951.690.23990.67410.2602-0.3537-0.2248-0.053-0.3208-0.2652-0.00130.40670.1016-0.05370.49980.02020.2919-46.243437.038713.1662
71.0914-0.1196-1.26921.3051-0.27980.93830.27390.71640.4167-0.2614-0.12880.0751-0.3274-0.09170.02260.37460.1483-0.00640.49140.04410.4158-63.599846.713921.1824
81.7134-1.2361-0.58372.97821.38251.97250.21730.04890.3656-0.37510.1013-0.7618-0.23770.23560.04790.2539-0.09110.04540.2761-0.02390.4903-11.202830.989617.3145
93.0385-0.3184-0.84171.23680.39731.74240.1202-0.32910.40890.0514-0.075-0.018-0.17450.04470.00070.3022-0.0207-0.02790.3368-0.05830.3197-35.649337.881834.4332
100.5977-0.1655-0.70161.73570.95920.81950.0764-0.18850.3608-0.12050.1424-0.4201-0.28990.04970.01220.2895-0.05490.00620.3249-0.04810.5114-16.40236.285525.1923
113.4487-0.074-0.89983.079-1.08932.2333-0.3328-0.0608-1.15850.18430.10790.37210.2543-0.1918-0.03750.33350.08740.05950.29690.15030.749-39.8653-32.848638.3617
122.70920.283-0.24882.34-1.06722.1897-0.1346-0.0614-0.2120.1532-0.1006-0.31680.09240.30650.00020.29620.04720.00490.29170.09290.311-22.9158-10.655725.0524
132.0409-0.0074-1.37790.6985-0.34710.76780.0447-0.0405-1.179-0.03820.0098-0.0329-0.11680.08540.01360.4340.09830.02380.41130.15750.7503-30.2662-27.861935.3894
143.42250.12720.08443.5227-0.85311.03090.2353-0.54750.50910.6971-0.02790.4574-0.2450.14960.13270.448-0.02560.1040.5365-0.37380.0916-70.917829.535859.404
151.30250.0019-0.49232.72690.41241.9032-0.4583-0.6248-0.40820.5510.244-0.08970.54530.3711-0.00690.49430.1848-0.00970.5280.05390.2915-63.31840.382954.5087
160.41430.0696-0.52561.6755-0.48930.43950.1029-0.4469-0.09340.63280.0715-0.11890.11190.09030.00690.56490.0361-0.01430.6043-0.12140.2668-68.854419.335662.4968
171.8869-0.0728-0.94443.9930.51851.7099-0.1025-0.0727-0.36580.303-0.02910.04960.1822-0.0884-0.00320.3334-0.0961-0.020.2619-0.0380.4318-72.8993-26.290932.2769
182.1437-0.60620.31282.61140.52851.6136-0.1408-0.0376-0.1169-0.0979-0.0150.39490.0355-0.23210.00040.373-0.0042-0.01230.2948-0.08920.3141-78.00843.52436.1391
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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