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- PDB-8aep: Reductase domain of the carboxylate reductase of Neurospora crassa -

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Basic information

Entry
Database: PDB / ID: 8aep
TitleReductase domain of the carboxylate reductase of Neurospora crassa
ComponentsAcetyl-CoA synthetase-like protein
KeywordsOXIDOREDUCTASE / Oxidereductase / Carboxylate reductase
Function / homology
Function and homology information


cellular biosynthetic process / :
Similarity search - Function
Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site ...Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Acetyl-CoA synthetase-like protein
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDaniel, B. / Schrufer, A. / Marlene, L. / Sagmeister, T. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Acs Catalysis / Year: 2022
Title: Structure of the Reductase Domain of a Fungal Carboxylic Acid Reductase and Its Substrate Scope in Thioester and Aldehyde Reduction.
Authors: Daniel, B. / Hashem, C. / Leithold, M. / Sagmeister, T. / Tripp, A. / Stolterfoht-Stock, H. / Messenlehner, J. / Keegan, R. / Winkler, C.K. / Ling, J.G. / Younes, S.H.H. / Oberdorfer, G. / ...Authors: Daniel, B. / Hashem, C. / Leithold, M. / Sagmeister, T. / Tripp, A. / Stolterfoht-Stock, H. / Messenlehner, J. / Keegan, R. / Winkler, C.K. / Ling, J.G. / Younes, S.H.H. / Oberdorfer, G. / Abu Bakar, F.D. / Gruber, K. / Pavkov-Keller, T. / Winkler, M.
History
DepositionJul 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
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 / _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
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA synthetase-like protein
B: Acetyl-CoA synthetase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0686
Polymers89,8052
Non-polymers2634
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-51 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.235, 137.487, 66.513
Angle α, β, γ (deg.)90.000, 112.333, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 650 - 1052 / Label seq-ID: 1 - 403

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Acetyl-CoA synthetase-like protein


Mass: 44902.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: GE21DRAFT_9612 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0DIR3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: Crystals were grown by mixing 0.5 microL 0.2 M ammonia sulphate, 0.1 M BisTRIS pH 5.5 and 25 percent PEG 3350 with 0.5 microL 18.00 mg per mL NcCAR R-domain in 50 mM MES buffer pH pH 7.0 ...Details: Crystals were grown by mixing 0.5 microL 0.2 M ammonia sulphate, 0.1 M BisTRIS pH 5.5 and 25 percent PEG 3350 with 0.5 microL 18.00 mg per mL NcCAR R-domain in 50 mM MES buffer pH pH 7.0 containing 10 mM magnesium chloride, 150 mM sodium chloride and 1 mM DTT. Crystals appeared after 6-9 weeks under vapor batch conditions.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.3→48.651 Å / Num. obs: 41333 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.171 / Rrim(I) all: 0.257 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-48.653.50.0557320.9950.050.075
2.3-2.383.90.70440590.6360.6310.949

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSP

5msp


Resolution: 2.3→48.651 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.074 / SU ML: 0.211 / Cross valid method: FREE R-VALUE / ESU R: 0.366 / ESU R Free: 0.255
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2586 2039 4.937 %
Rwork0.2002 39260 -
all0.203 --
obs-41299 99.614 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.551 Å2-0 Å2-1.231 Å2
2--0.075 Å2-0 Å2
3---0.288 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6206 0 12 741 6959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136356
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155932
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6398636
X-RAY DIFFRACTIONr_angle_other_deg1.2671.5813712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21622.625320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.175151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9381538
X-RAY DIFFRACTIONr_chiral_restr0.0680.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021410
X-RAY DIFFRACTIONr_nbd_refined0.1930.21339
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.25401
X-RAY DIFFRACTIONr_nbtor_refined0.1560.23059
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2471
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1530.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.211
X-RAY DIFFRACTIONr_nbd_other0.2460.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3270.224
X-RAY DIFFRACTIONr_mcbond_it2.4282.5653164
X-RAY DIFFRACTIONr_mcbond_other2.4272.5653163
X-RAY DIFFRACTIONr_mcangle_it3.9153.8353948
X-RAY DIFFRACTIONr_mcangle_other3.9153.8353949
X-RAY DIFFRACTIONr_scbond_it2.7692.9363192
X-RAY DIFFRACTIONr_scbond_other2.7642.9323184
X-RAY DIFFRACTIONr_scangle_it4.6084.264688
X-RAY DIFFRACTIONr_scangle_other4.6034.2534676
X-RAY DIFFRACTIONr_lrange_it6.99730.6577382
X-RAY DIFFRACTIONr_lrange_other6.86230.3927240
X-RAY DIFFRACTIONr_ncsr_local_group_10.0850.0512849
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.085180.05008
12BX-RAY DIFFRACTIONLocal ncs0.085180.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.3191540.26829130.2730720.7850.79699.83720.252
2.36-2.4240.3251260.25228200.25529540.80.8399.72920.236
2.424-2.4940.291280.24427340.24628700.8260.84699.72130.227
2.494-2.5710.3381290.22327000.22828340.8250.86899.82360.205
2.571-2.6550.2961360.22626040.2327490.8560.88199.67260.205
2.655-2.7480.2391180.21824960.21926210.8770.88399.73290.199
2.748-2.8510.3061200.20124100.20625410.8560.90299.56710.184
2.851-2.9670.2821420.19122870.19724380.8890.91699.63080.175
2.967-3.0990.2841370.20722010.21123440.8840.91299.7440.194
3.099-3.2490.271940.20421500.20722510.8930.92499.6890.193
3.249-3.4240.2871190.21120130.21521390.8940.9399.67270.203
3.424-3.6310.2651170.20419170.20820390.9260.93599.75480.197
3.631-3.880.2091190.17517510.17718790.9320.95299.5210.169
3.88-4.1880.218760.16117020.16317880.940.95699.44070.154
4.188-4.5850.192910.14915300.15216370.9480.95899.02260.144
4.585-5.120.186710.1614230.16115050.9480.95699.26910.154
5.12-5.9010.24510.18312390.18512960.9390.95499.5370.175
5.901-7.2010.266510.21210580.21411130.9090.93499.64060.203
7.201-10.0740.259320.1888370.198740.9340.95399.42790.188
10.074-48.6510.19280.2334750.2315100.9570.95198.62740.237

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