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- PDB-2ph3: Crystal structure of 3-oxoacyl-[acyl carrier protein] reductase T... -

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Basic information

Entry
Database: PDB / ID: 2ph3
TitleCrystal structure of 3-oxoacyl-[acyl carrier protein] reductase TTHA0415 from Thermus thermophilus
Components3-oxoacyl-[acyl carrier protein] reductase
KeywordsOXIDOREDUCTASE / TTHA0415 / Thermus thermophilus / STRUCTURAL GENOMICS / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / PSI / Protein Structure Initiative
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / 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
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsSwindell II, J.T. / Chen, L. / Zhu, J. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Chrzas, J. / Rose, J.P. ...Swindell II, J.T. / Chen, L. / Zhu, J. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Chrzas, J. / 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 3-oxoacyl-[acyl carrier protein] reductase TTHA0415 from Thermus thermophilus
Authors: Swindell II, J.T. / Chen, L. / Zhu, J. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Chrzas, J. / Rose, J.P. / Wang, B.C.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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)52,4862
Polymers52,4862
Non-polymers00
Water3,387188
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)104,9724
Polymers104,9724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area12870 Å2
ΔGint-72 kcal/mol
Surface area34230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.525, 76.525, 137.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe biological assembly is a tetramer

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Components

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


Mass: 26243.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8, DSM 579 / Gene: TTHA0415 / Plasmid: pET-11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5SL78, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (9.5 mg/ml) AND SOLUTION CONTAINING 0.1 M Tris-HCl pH 8.5, 2.4 M di-Ammonium Phosphate, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionRedundancy: 20.8 % / Av σ(I) over netI: 22.8 / Number: 733560 / Rmerge(I) obs: 0.065 / Χ2: 1.47 / D res high: 1.91 Å / D res low: 50 Å / Num. obs: 35274 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.115099.510.0511.73122.6
3.274.1110010.0662.4222.7
2.853.2710010.061.61721.7
2.592.8510010.0631.40721.1
2.412.5910010.0681.30520.8
2.262.4110010.0731.30420.4
2.152.2610010.0821.23820.2
2.062.1510010.0961.19319.9
1.982.0610010.1181.16119.7
1.911.9810010.1441.15318.9
ReflectionResolution: 1.91→50 Å / Num. obs: 35274 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 20.8 % / Rsym value: 0.065 / Χ2: 1.474 / Net I/σ(I): 22.8
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.144 / Num. unique all: 3504 / Χ2: 1.153 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
SGXPROphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HQ1

2hq1


Resolution: 1.91→19.67 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.374 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.152
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1763 5 %RANDOM
Rwork0.189 ---
all0.191 35198 --
obs0.191 35198 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.91→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 0 188 3809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223667
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9714954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99323.248157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81615635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.751538
X-RAY DIFFRACTIONr_chiral_restr0.110.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022731
X-RAY DIFFRACTIONr_nbd_refined0.2330.21827
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2810.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.220
X-RAY DIFFRACTIONr_mcbond_it1.4341.52457
X-RAY DIFFRACTIONr_mcangle_it1.54523770
X-RAY DIFFRACTIONr_scbond_it2.71431339
X-RAY DIFFRACTIONr_scangle_it4.2474.51184
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 129 -
Rwork0.2 2452 -
obs-2581 100 %

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