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

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Basic information

Entry
Database: PDB / ID: 6jzq
TitleThe crystal structure of acyl-acyl carrier protein (acyl-ACP) reductase (AAR)
ComponentsLong-chain acyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / reductase / alkane / aldehyde / oxygenase
Function / homologylong-chain acyl-[acyl-carrier-protein] reductase / Long-chain acyl-[acyl-carrier-protein] reductase / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Long-chain acyl-[acyl-carrier-protein] reductase
Function and homology information
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.798 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Long-chain acyl-[acyl-carrier-protein] reductase
B: Long-chain acyl-[acyl-carrier-protein] reductase
C: Long-chain acyl-[acyl-carrier-protein] reductase
D: Long-chain acyl-[acyl-carrier-protein] reductase
E: Long-chain acyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)191,5595
Polymers191,5595
Non-polymers00
Water86548
1
A: Long-chain acyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)38,3121
Polymers38,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Long-chain acyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)38,3121
Polymers38,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Long-chain acyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)38,3121
Polymers38,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Long-chain acyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)38,3121
Polymers38,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Long-chain acyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)38,3121
Polymers38,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.167, 201.442, 124.580
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 38311.707 Da / Num. of mol.: 5
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 0.1M Tris-HCl, pH8.5, 1.2M NaAc

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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 S 6M / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.798→46.111 Å / Num. obs: 53286 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.03 / Rsym value: 0.093 / Net I/σ(I): 23.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 5161 / CC1/2: 0.885 / Rpim(I) all: 0.3 / Rsym value: 0.86

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.798→46.111 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1995 3.75 %
Rwork0.2177 --
obs0.2191 53173 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→46.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12927 0 0 48 12975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213195
X-RAY DIFFRACTIONf_angle_d1.48317926
X-RAY DIFFRACTIONf_dihedral_angle_d22.3254633
X-RAY DIFFRACTIONf_chiral_restr0.0752055
X-RAY DIFFRACTIONf_plane_restr0.0092324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7981-2.86810.33711350.32893453X-RAY DIFFRACTION94
2.8681-2.94560.33251410.31793648X-RAY DIFFRACTION99
2.9456-3.03230.34171420.30983648X-RAY DIFFRACTION99
3.0323-3.13010.34241430.28923660X-RAY DIFFRACTION99
3.1301-3.2420.29391430.28263672X-RAY DIFFRACTION99
3.242-3.37170.36591420.27163658X-RAY DIFFRACTION99
3.3717-3.52510.30471430.25553655X-RAY DIFFRACTION99
3.5251-3.71090.30071430.24363669X-RAY DIFFRACTION99
3.7109-3.94330.28741420.21723669X-RAY DIFFRACTION99
3.9433-4.24760.22231440.20083685X-RAY DIFFRACTION100
4.2476-4.67470.21221430.19033655X-RAY DIFFRACTION100
4.6747-5.35020.20451440.18733701X-RAY DIFFRACTION99
5.3502-6.73730.25161440.1993667X-RAY DIFFRACTION99
6.7373-46.11690.19831460.16423738X-RAY DIFFRACTION99

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