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- PDB-2p68: Crystal Structure of aq_1716 from Aquifex Aeolicus VF5 -

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Basic information

Entry
Database: PDB / ID: 2p68
TitleCrystal Structure of aq_1716 from Aquifex Aeolicus VF5
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / aq_1716 / 3-ketoacyl-acyl carrier protein reductase / 3-oxoacyl-[acyl-carrier-protein] reductase / Aquifex aeolicus VF5 / structural genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsChen, L. / Chen, L.-Q. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Dillard, B. / Rose, J.P. / Wang, B.-C. ...Chen, L. / Chen, L.-Q. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Dillard, B. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of aq_1716 from Aquifex aeolicus VF5
Authors: Chen, L. / Chen, L.-Q. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Dillard, B. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,7922
Polymers53,7922
Non-polymers00
Water9,206511
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase

A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)107,5844
Polymers107,5844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12190 Å2
ΔGint-92 kcal/mol
Surface area35700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.698, 64.214, 73.448
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

21A-431-

HOH

31B-270-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase / 3-ketoacyl-acyl carrier protein reductase


Mass: 26896.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: fabG, aq_1716 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: O67610, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: USING 4 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.8 mg/ml) AND RESERVOIR SOLUTION CONTAINING 45% v/v PEG200, 0.1M Tris-HCl (pH 6.4), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2006 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionRedundancy: 23.7 % / Av σ(I) over netI: 20.3 / Number: 1034615 / Rmerge(I) obs: 0.089 / Χ2: 3.02 / D res high: 1.84 Å / D res low: 50 Å / Num. obs: 43626 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.995099.710.0663.05327.5
3.163.9910010.0743.6928.6
2.763.1610010.0863.53828.7
2.512.7610010.1043.23229.1
2.332.5110010.1213.629
2.192.3310010.1393.13628.7
2.082.1910010.1642.51127.2
1.992.0899.910.1681.53313.5
1.921.9999.510.2081.38912.7
1.841.9298.210.2661.9811.1
ReflectionResolution: 1.84→50 Å / Num. all: 43626 / Num. obs: 43626 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 23.7 % / Rsym value: 0.089 / Χ2: 3.016 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.84-1.9211.10.26641981.98198.2
1.92-1.9912.70.20842971.389199.5
1.99-2.0813.50.16843131.533199.9
2.08-2.1927.20.16443022.5111100
2.19-2.3328.70.13943523.1361100
2.33-2.51290.12143353.61100
2.51-2.7629.10.10443723.2321100
2.76-3.1628.70.08643913.5381100
3.16-3.9928.60.07444323.691100
3.99-5027.50.06646343.053199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C07

2c07


Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.484 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2186 5 %RANDOM
Rwork0.183 ---
obs0.185 43574 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.301 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--0.58 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 0 511 4194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223727
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9695030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4735481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38124.863146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58215690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0931520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022683
X-RAY DIFFRACTIONr_nbd_refined0.1980.21873
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.260
X-RAY DIFFRACTIONr_mcbond_it0.651.52461
X-RAY DIFFRACTIONr_mcangle_it1.03323831
X-RAY DIFFRACTIONr_scbond_it1.89831427
X-RAY DIFFRACTIONr_scangle_it3.0864.51199
LS refinement shellResolution: 1.84→1.891 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 138 -
Rwork0.202 2833 -
obs-2971 92.79 %

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