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- PDB-2a4k: 3-Oxoacyl-[acyl carrier protein] reductase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 2a4k
Title3-Oxoacyl-[acyl carrier protein] reductase from Thermus thermophilus TT0137
Components3-oxoacyl-[acyl carrier protein] reductase
KeywordsOXIDOREDUCTASE / reductase / hyperthermophile / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
AuthorsZhou, W. / Ebihara, A. / Tempel, W. / Yokoyama, S. / Chen, L. / Kuramitsu, S. / Nguyen, J. / Chang, S.-H. / Liu, Z.-J. / Rose, J.P. ...Zhou, W. / Ebihara, A. / Tempel, W. / Yokoyama, S. / Chen, L. / Kuramitsu, S. / Nguyen, J. / Chang, S.-H. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: 3-Oxoacyl-[acyl carrier protein] reductase from Thermus thermophilus TT0137
Authors: Zhou, W. / Ebihara, A. / Tempel, W. / Yokoyama, S. / Chen, L. / Kuramitsu, S. / Nguyen, J. / Chang, S.-H. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C.
History
DepositionJun 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)54,10630
Polymers54,1062
Non-polymers028
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-24 kcal/mol
Surface area18770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.013, 91.565, 54.847
Angle α, β, γ (deg.)90.00, 104.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27053.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria)
References: GenBank: 55978203, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 28 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.8 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 5.5
Details: 0.1M citrate, 30v/v% 1,4-butanediol, pH 5.5, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→53.19 Å / Num. obs: 118284 / Scaling rejects: 2538

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.55 / Cor.coef. Fo:Fc: 0.213
Highest resolutionLowest resolution
Translation4 Å15 Å
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.37-10019.40.58507
6.62-8.3711.50.704513
5.77-6.6211.10.656507
5.23-5.7710.80.688521
4.82-5.2310.40.727536
4.49-4.8210.30.783597
4.23-4.4912.50.757630
4-4.2311.50.746693
3.81-414.10.724708
3.64-3.8110.80.763729
3.5-3.64110.741780
3.36-3.511.90.721810
3.25-3.36140.635807
3.14-3.2513.40.597882
3.05-3.1413.60.595868
2.96-3.0511.60.6957
2.88-2.9613.80.598945
2.8-2.8812.20.61945
2.74-2.811.90.6491004
2.67-2.7412.30.6351040
2.61-2.6712.90.6321030
2.56-2.6112.40.6271076
2.5-2.5612.50.651066
2.45-2.512.50.6361140
2.41-2.4513.60.6371067
2.36-2.4116.30.5891058
2.29-2.36180.5861263

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Processing

Software
NameVersionClassificationNB
3DSCALEdata processing
EPMR2.5phasing
DM5phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.401data extraction
LSCALEdata scaling
ARP/wARPmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1uls

1uls


Resolution: 2.301→46.078 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.221 / SU B: 5.821 / SU ML: 0.15 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.223
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Other software used in refinement are arp, warp and molprobity.
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 713 3.146 %THIN SHELLS
Rwork0.2145 ---
all0.216 ---
obs-22665 96.624 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.364 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20 Å2-0.003 Å2
2--0.048 Å20 Å2
3----0.054 Å2
Refinement stepCycle: LAST / Resolution: 2.301→46.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 28 60 3203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223155
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9844282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9365433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19623.67109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02515484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2871521
X-RAY DIFFRACTIONr_chiral_restr0.0750.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022322
X-RAY DIFFRACTIONr_nbd_refined0.1850.21245
X-RAY DIFFRACTIONr_nbtor_refined0.2820.22133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.210
X-RAY DIFFRACTIONr_mcbond_it1.9322225
X-RAY DIFFRACTIONr_mcangle_it2.93833363
X-RAY DIFFRACTIONr_scbond_it2.10821059
X-RAY DIFFRACTIONr_scangle_it3.0993919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.301-2.3610.217310.1831138173067.572
2.361-2.4250.265620.1821504169592.389
2.425-2.4950.255310.1791549161497.893
2.495-2.5720.245620.181498156699.617
2.572-2.6560.238620.191470154199.416
2.656-2.7490.266310.1951485151899.868
2.749-2.8520.3550.21213701425100
2.852-2.9680.344380.2471349139199.712
2.968-3.0990.201310.2561277131299.695
3.099-3.250.28620.2631242130599.923
3.25-3.4250.252310.2431164119799.833
3.425-3.6310.246310.1961102113899.561
3.631-3.880.162310.2111032107299.16
3.88-4.1890.289310.205985102599.122
4.189-4.5850.256310.19489793099.785
4.585-5.120.272310.20178982699.274
5.12-5.90.279310.24169773399.318
5.9-7.19600.27363663799.843
7.196-10.0550.163310.20247150499.603
10.055-46.07800.27629729899.664

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