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- PDB-6zn4: MaeB malic enzyme domain apoprotein -

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Basic information

Entry
Database: PDB / ID: 6zn4
TitleMaeB malic enzyme domain apoprotein
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
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, 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
Similarity search - Domain/homology
NADP-dependent malate dehydrogenase / Malate dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 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 / Polymer sequence / Refinement description / 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 / exptl_crystal / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / 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 / _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 / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_conn.ptnr1_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _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 / _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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,2604
Polymers96,2122
Non-polymers492
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-92 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.028, 92.654, 96.956
Angle α, β, γ (deg.)90.000, 91.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48105.859 Da / Num. of mol.: 2
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+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 9.3 / Details: 0.1M bicine pH 9.3 25% w/v PEG smear medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.67→48.019 Å / Num. obs: 96511 / % possible obs: 97.8 % / Redundancy: 6.81 % / CC1/2: 0.99 / Net I/σ(I): 10.81
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 4697 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CEE

5cee


Resolution: 1.679→48.019 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 4646 4.93 %
Rwork0.1702 89526 -
obs0.1718 94172 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.99 Å2 / Biso mean: 36.9767 Å2 / Biso min: 8.37 Å2
Refinement stepCycle: final / Resolution: 1.679→48.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6115 0 2 680 6797
Biso mean--24.71 43.68 -
Num. residues----814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076235
X-RAY DIFFRACTIONf_angle_d1.1098443
X-RAY DIFFRACTIONf_chiral_restr0.046969
X-RAY DIFFRACTIONf_plane_restr0.0051106
X-RAY DIFFRACTIONf_dihedral_angle_d13.3742317
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6791-1.69820.39151200.3362284292
1.6982-1.71820.34621230.3149294295
1.7182-1.73910.35611340.2941294696
1.7391-1.76110.31141390.2693291795
1.7611-1.78430.27041550.2587291896
1.7843-1.80870.23811370.2501292596
1.8087-1.83460.30351650.2379291895
1.8346-1.8620.24021470.2245295597
1.862-1.89110.22231600.218292196
1.8911-1.92210.23911700.2033291195
1.9221-1.95520.22771680.195297899
1.9552-1.99080.2031390.1867297996
1.9908-2.02910.23141200.1904301898
2.0291-2.07050.24261370.1946295997
2.0705-2.11550.22321380.1835301998
2.1155-2.16470.20441520.1833298098
2.1647-2.21880.19561690.1733299398
2.2188-2.27880.20781870.1721296597
2.2788-2.34590.21831450.1724301099
2.3459-2.42160.19921770.1719298397
2.4216-2.50810.19521750.166301699
2.5081-2.60860.2211670.1718299999
2.6086-2.72730.19661970.1647297298
2.7273-2.8710.20841790.1741299999
2.871-3.05090.2141680.1652303299
3.0509-3.28640.20211380.1653307699
3.2864-3.6170.19291740.1557305299
3.617-4.14020.16831630.135305399
4.1402-5.21520.1641480.12853110100
5.2152-48.0190.16441550.1421313899
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)
10.1112-0.14030.01190.17910.02340.6731-0.0185-0.06550.12670.13080.01830.0518-0.09620.0197-0.20570.175-0.00040.04990.1454-0.11520.2995-8.05238.91525.812
20.06010.02090.03150.01140.0160.03750.0030.01670.0455-0.05210.0573-0.05430.03290.2664-00.12160.00380.00350.2035-0.02580.208918.11624.7888.634
30.12880.0036-0.15320.1579-0.12830.3996-0.042-0.22680.00090.1149-0.01770.06970.16420.0367-0.00120.1678-0.00570.01370.1976-0.02610.1462-4.36715.97226.529
40.0112-0.02160.01340.054-0.01780.0230.02-0.1068-0.13690.1281-0.03130.08160.1583-0.14530.00050.3862-0.02590.01490.52430.06730.1997-11.5465.66848.944
50.01650.0093-0.00680.03050.01360.01550.0841-0.098-0.2002-0.05770.030.09650.1436-0.12250.00010.5077-0.0998-0.07210.57010.0060.4519-23.9661.54841.905
60.0542-0.0780.080.4906-0.05640.12920.1106-0.14370.05030.210.00320.2841-0.1199-0.31560.04560.4569-0.00430.14490.6903-0.03040.2592-18.86917.76454.487
70.2173-0.04830.0570.0189-0.02850.04560.0689-0.29810.03590.0854-0.0456-0.0379-0.08310.2692-0.00270.2847-0.02230.00390.4706-0.03390.12421.48321.12144.88
80.05040.0522-0.05470.0759-0.05190.06080.0838-0.2691-0.07470.0021-0.1301-0.11090.05680.2757-0.00540.27370.0923-0.04970.453-0.00430.17811.18412.37737.75
90.47160.0477-0.12970.1762-0.17360.18620.0378-0.11330.00630.02030.006-0.0733-0.0140.12410.08610.06460.0144-0.01580.2298-0.05590.1820.17124.0814.572
100.26010.1262-0.19630.5131-0.09390.3950.0045-0.02630.0776-0.08210.00070.07070.0139-0.05020.05060.1068-0.0019-0.01920.0932-0.02840.1308-1.96425.1638.492
110.2547-0.1033-0.09560.3091-0.33260.5568-0.05080.2684-0.2757-0.70270.0633-0.19550.4231-0.01210.26210.751-0.02310.05980.2426-0.11430.31636.4620.931-22.413
120.16440.12070.02420.0890.02130.05560.0010.1483-0.0819-0.34060.026-0.43050.04280.18040.11150.36170.07340.19490.217-0.0190.383119.48329.831-16.371
130.0056-0.0339-0.01180.516-0.20910.27640.03610.04330.0244-0.10950.01830.0545-0.1082-0.02380.06820.1537-0.0001-0.01650.10220.01990.18893.37240.11-3.804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:37 )A16 - 37
2X-RAY DIFFRACTION2( CHAIN A AND RESID 38:65 )A38 - 65
3X-RAY DIFFRACTION3( CHAIN A AND RESID 66:193 )A66 - 193
4X-RAY DIFFRACTION4( CHAIN A AND RESID 194:232 )A194 - 232
5X-RAY DIFFRACTION5( CHAIN A AND RESID 233:261 )A233 - 261
6X-RAY DIFFRACTION6( CHAIN A AND RESID 262:321 )A262 - 321
7X-RAY DIFFRACTION7( CHAIN A AND RESID 322:398 )A322 - 398
8X-RAY DIFFRACTION8( CHAIN A AND RESID 399:421 )A399 - 421
9X-RAY DIFFRACTION9( CHAIN B AND RESID 15:37 )B15 - 37
10X-RAY DIFFRACTION10( CHAIN B AND RESID 38:193 )B38 - 193
11X-RAY DIFFRACTION11( CHAIN B AND RESID 194:287 )B194 - 287
12X-RAY DIFFRACTION12( CHAIN B AND RESID 288:331 )B288 - 331
13X-RAY DIFFRACTION13( CHAIN B AND RESID 332:422 )B332 - 422

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