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- PDB-6jzy: Crystal structure of AAR with NADPH and stearyl in complex with A... -

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Basic information

Entry
Database: PDB / ID: 6jzy
TitleCrystal structure of AAR with NADPH and stearyl in complex with ADO binding a long chain carbohydrate
Components
  • Aldehyde decarbonylase
  • Long-chain acyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE/LYASE / reductase / alkane / aldehyde / oxygenase / OXIDOREDUCTASE-LYASE complex
Function / homology
Function and homology information


long-chain acyl-[acyl-carrier-protein] reductase / aldehyde oxygenase (deformylating) activity / aldehyde oxygenase (deformylating) / transition metal ion binding / oxidoreductase activity
Similarity search - Function
Long-chain acyl-[acyl-carrier-protein] reductase / Long-chain fatty aldehyde decarbonylase / Long-chain fatty aldehyde decarbonylase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle ...Long-chain acyl-[acyl-carrier-protein] reductase / Long-chain fatty aldehyde decarbonylase / Long-chain fatty aldehyde decarbonylase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-NDP / octadecanal / HEXADECAN-1-OL / Long-chain acyl-[acyl-carrier-protein] reductase / Aldehyde decarbonylase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, H.M. / Li, M. / Gao, Y.
Funding support China, 6items
OrganizationGrant numberCountry
Chinese Academy of SciencesKey Research Program of Frontier Sciences QYZDB-SSW-SMC005 China
Chinese Academy of SciencesStrategic Priority Research Program XDB27020106 China
Chinese Academy of SciencesStrategic Priority Research Program XDB08020302 China
National Natural Science Foundation of China31770778 China
Ministry of Science and Technology (China)National Key R&D Program of China 2017YFA0503702 China
Ministry of Science and Technology (China)National Key R&D Program of China 2011CBA00900 China
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into catalytic mechanism and product delivery of cyanobacterial acyl-acyl carrier protein reductase.
Authors: Gao, Y. / Zhang, H. / Fan, M. / Jia, C. / Shi, L. / Pan, X. / Cao, P. / Zhao, X. / Chang, W. / Li, M.
History
DepositionMay 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Long-chain acyl-[acyl-carrier-protein] reductase
B: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6797
Polymers67,3112
Non-polymers1,3685
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-33 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.609, 71.248, 135.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Long-chain acyl-[acyl-carrier-protein] reductase / Acyl-ACP reductase


Mass: 38311.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Gene: Synpcc7942_1594, SEC0028 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q54765, long-chain acyl-[acyl-carrier-protein] reductase
#2: Protein Aldehyde decarbonylase / AD / Fatty aldehyde decarbonylase


Mass: 28998.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Gene: SEC0027 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8KPT4, aldehyde oxygenase (deformylating)

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Non-polymers , 5 types, 148 molecules

#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OCD / octadecanal


Mass: 268.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PL3 / HEXADECAN-1-OL


Mass: 242.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 0.1M HEPES, pH 7.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.43 Å / Num. obs: 37640 / % possible obs: 99.1 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rsym value: 0.074 / Net I/σ(I): 32
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.99 / Num. unique obs: 3664 / CC1/2: 0.87 / Rpim(I) all: 0.28

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RC8

4rc8


Resolution: 2.1→49.13 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.04
RfactorNum. reflection% reflection
Rfree0.2352 2007 5.34 %
Rwork0.1956 --
obs0.1978 37568 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 86 143 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074529
X-RAY DIFFRACTIONf_angle_d0.996134
X-RAY DIFFRACTIONf_dihedral_angle_d7.0783671
X-RAY DIFFRACTIONf_chiral_restr0.054677
X-RAY DIFFRACTIONf_plane_restr0.005797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0992-2.15170.31021340.27842255X-RAY DIFFRACTION90
2.1517-2.20990.29721510.25812504X-RAY DIFFRACTION100
2.2099-2.27490.32851230.24562533X-RAY DIFFRACTION100
2.2749-2.34830.28781400.23132515X-RAY DIFFRACTION99
2.3483-2.43230.26931530.2212525X-RAY DIFFRACTION99
2.4323-2.52970.29451420.22782527X-RAY DIFFRACTION100
2.5297-2.64480.29081420.23122528X-RAY DIFFRACTION100
2.6448-2.78420.29461550.22562515X-RAY DIFFRACTION100
2.7842-2.95860.25441350.23442573X-RAY DIFFRACTION100
2.9586-3.1870.29341430.22862539X-RAY DIFFRACTION100
3.187-3.50770.23961360.21272581X-RAY DIFFRACTION100
3.5077-4.0150.22641470.18592602X-RAY DIFFRACTION100
4.015-5.05770.19771500.15912630X-RAY DIFFRACTION100
5.0577-49.14360.19111560.16552734X-RAY DIFFRACTION100

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