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- PDB-6jzu: The crystal structure of acyl-acyl carrier protein (acyl-ACP) red... -

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Basic information

Entry
Database: PDB / ID: 6jzu
TitleThe crystal structure of acyl-acyl carrier protein (acyl-ACP) reductase (AAR) in complex with aldehyde deformylating oxygenase (ADO)
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) / : / : / fatty acid elongation / transition metal ion binding / oxidoreductase activity / cytosol
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 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 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: 2.181 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 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)67,1386
Polymers66,5162
Non-polymers6234
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-30 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.377, 71.313, 137.137
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: 37516.859 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 / 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 , 4 types, 167 molecules

#3: Chemical ChemComp-OCD / octadecanal


Mass: 268.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
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: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→49.43 Å / Num. obs: 34553 / % possible obs: 99.6 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rsym value: 0.089 / Net I/σ(I): 30
Reflection shellResolution: 2.18→2.26 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 1708 / CC1/2: 0.76 / Rpim(I) all: 0.31 / Rsym value: 1.14

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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: 2.181→49.427 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1996 5.82 %
Rwork0.2035 --
obs0.2064 34322 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.181→49.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 38 163 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084460
X-RAY DIFFRACTIONf_angle_d0.8576029
X-RAY DIFFRACTIONf_dihedral_angle_d6.2523636
X-RAY DIFFRACTIONf_chiral_restr0.05669
X-RAY DIFFRACTIONf_plane_restr0.005786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1811-2.23570.32251200.2662108X-RAY DIFFRACTION92
2.2357-2.29610.29471460.25192244X-RAY DIFFRACTION98
2.2961-2.36370.28291450.24432271X-RAY DIFFRACTION99
2.3637-2.440.3141410.23462279X-RAY DIFFRACTION100
2.44-2.52720.32051500.23652281X-RAY DIFFRACTION100
2.5272-2.62830.26531370.23242323X-RAY DIFFRACTION100
2.6283-2.7480.25441470.21822294X-RAY DIFFRACTION100
2.748-2.89280.29211420.22492298X-RAY DIFFRACTION100
2.8928-3.0740.2881360.22472319X-RAY DIFFRACTION100
3.074-3.31130.27281430.21232327X-RAY DIFFRACTION100
3.3113-3.64450.27461430.20162337X-RAY DIFFRACTION100
3.6445-4.17160.2361500.17972368X-RAY DIFFRACTION100
4.1716-5.25480.2081430.16672372X-RAY DIFFRACTION100
5.2548-49.43970.19521530.17512505X-RAY DIFFRACTION100

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