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- PDB-6zn7: MaeB malic enzyme domain apoprotein -

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Basic information

Entry
Database: PDB / ID: 6zn7
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 / 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, 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, 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 NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent malate dehydrogenase / Malate dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 / Data collection / Database references / Derived calculations / 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 / pdbx_nonpoly_scheme / 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 / pdbx_validate_symm_contact / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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.pdbx_description / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num / _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 / _pdbx_validate_symm_contact.auth_seq_id_1 / _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_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)97,7476
Polymers96,2122
Non-polymers1,5354
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-97 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.817, 92.192, 95.796
Angle α, β, γ (deg.)90.000, 91.130, 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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 9.3 / Details: 0.1M Bicine pH 9.3 25% 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: 0.97633 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.67→95.78 Å / Num. obs: 96099 / % possible obs: 99.9 % / Redundancy: 6.52 % / CC1/2: 0.99 / Net I/σ(I): 6.87
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 4736 / CC1/2: 0.47

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Processing

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

5cee


Resolution: 1.67→95.777 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 4763 5.07 %
Rwork0.1794 89248 -
obs0.1813 94011 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.21 Å2 / Biso mean: 34.4667 Å2 / Biso min: 10.14 Å2
Refinement stepCycle: final / Resolution: 1.67→95.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 98 617 6856
Biso mean--41.89 41.13 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076365
X-RAY DIFFRACTIONf_angle_d1.038641
X-RAY DIFFRACTIONf_chiral_restr0.043986
X-RAY DIFFRACTIONf_plane_restr0.0051118
X-RAY DIFFRACTIONf_dihedral_angle_d13.1152339
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6703-1.68930.3491430.3564279692
1.6893-1.70910.30041530.3329294695
1.7091-1.730.36181600.3215284796
1.73-1.75190.35351510.314289995
1.7519-1.77490.33661750.3027289095
1.7749-1.79920.3231580.2801287096
1.7992-1.82490.30931780.2791291296
1.8249-1.85220.32721530.2642295097
1.8522-1.88110.29011560.262287397
1.8811-1.9120.33611410.2636300497
1.912-1.9450.26671540.2501290297
1.945-1.98030.25341630.2195300298
1.9803-2.01840.23791770.2001290698
2.0184-2.05960.22661640.202299998
2.0596-2.10440.27321610.1889299699
2.1044-2.15340.21881860.1894296499
2.1534-2.20720.22061860.179300299
2.2072-2.26690.22142040.1795294298
2.2669-2.33360.2121650.1769296798
2.3336-2.40890.21761560.1745301299
2.4089-2.4950.20661670.1655299899
2.495-2.59490.20141320.1617304699
2.5949-2.71310.21071150.1616304298
2.7131-2.85610.23891310.1666304899
2.8561-3.03510.20811330.1671306299
3.0351-3.26940.19951330.16513076100
3.2694-3.59840.18272170.15632998100
3.5984-4.11910.16761710.14033042100
4.1191-5.18970.17121500.1343099100
5.1897-95.7770.1841300.14933158100
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)
11.14580.0352-0.4080.8001-0.14951.129-0.0168-0.25660.05460.1036-0.00290.01950.06010.04660.00820.13980.0036-0.01710.1775-0.02680.139744.59420.4119.454
20.99110.31730.25731.3436-0.56071.64910.1164-0.686-0.0550.3817-0.11150.2138-0.0617-0.1232-0.09190.32270.00390.02340.5964-0.03770.185437.53213.953142.396
30.80320.046-0.25470.8178-0.05170.9009-0.0015-0.09310.0613-0.04310.00860.0007-0.0002-0.0088-0.00930.12060.0029-0.01350.1188-0.01990.150647.01425.166105.227
41.04640.43-0.13342.8205-0.67761.6559-0.05010.2294-0.1133-0.68180.0336-0.31490.28290.0776-0.09480.30070.0150.03830.1419-0.00980.195553.62530.29882.246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:193 )A16 - 193
2X-RAY DIFFRACTION2( CHAIN A AND RESID 194:420 )A194 - 420
3X-RAY DIFFRACTION3( CHAIN B AND RESID 15:193 )B15 - 193
4X-RAY DIFFRACTION4( CHAIN B AND RESID 194:422 )B194 - 422

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