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- PDB-4rzi: Crystal structure of PhaB from Synechocystis sp. PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 4rzi
TitleCrystal structure of PhaB from Synechocystis sp. PCC 6803
Components3-ketoacyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase (SDR) family / AcAcCoA reductase
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
: / : / 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 ...: / : / 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
: / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.891 Å
AuthorsXue, S. / Liu, Y.
CitationJournal: Febs Lett. / Year: 2015
Title: Structure-directed construction of a high-performance version of the enzyme FabG from the photosynthetic microorganism Synechocystis sp. PCC 6803.
Authors: Liu, Y. / Feng, Y. / Cao, X. / Li, X. / Xue, S.
History
DepositionDec 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
B: 3-ketoacyl-acyl carrier protein reductase
A: 3-ketoacyl-acyl carrier protein reductase
C: 3-ketoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)76,0803
Polymers76,0803
Non-polymers00
Water00
1
B: 3-ketoacyl-acyl carrier protein reductase

B: 3-ketoacyl-acyl carrier protein reductase

B: 3-ketoacyl-acyl carrier protein reductase

B: 3-ketoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)101,4404
Polymers101,4404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area13390 Å2
ΔGint-87 kcal/mol
Surface area32630 Å2
MethodPISA
2
A: 3-ketoacyl-acyl carrier protein reductase
C: 3-ketoacyl-acyl carrier protein reductase

A: 3-ketoacyl-acyl carrier protein reductase
C: 3-ketoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)101,4404
Polymers101,4404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+2/31
Buried area13530 Å2
ΔGint-87 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.806, 122.806, 199.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein 3-ketoacyl-acyl carrier protein reductase


Mass: 25360.074 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: fabG, MYO_113190 / Production host: Escherichia coli (E. coli) / References: UniProt: M1M987, UniProt: P73826*PLUS

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.22M MgAC, 0.1M sodium cacodylater trihydrate pH6.5, 18%PEG8000 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0001 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 20301 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 42 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.89-2.94199
2.94-3.53199
3.53-4.591100
4.59-7.841100
7.84-50199.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.891→38.765 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1038 5.12 %RANDOM
Rwork0.2007 ---
all0.2031 20301 --
obs0.2031 20268 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.891→38.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 0 0 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015397
X-RAY DIFFRACTIONf_angle_d1.2537311
X-RAY DIFFRACTIONf_dihedral_angle_d12.3921947
X-RAY DIFFRACTIONf_chiral_restr0.078861
X-RAY DIFFRACTIONf_plane_restr0.008942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8908-3.04310.35311510.27872674X-RAY DIFFRACTION98
3.0431-3.23370.30391590.25662725X-RAY DIFFRACTION100
3.2337-3.48320.31751470.23562730X-RAY DIFFRACTION100
3.4832-3.83350.25731510.20532766X-RAY DIFFRACTION100
3.8335-4.38750.231480.18532781X-RAY DIFFRACTION100
4.3875-5.52530.19781480.16542804X-RAY DIFFRACTION99
5.5253-38.76830.18581340.16852750X-RAY DIFFRACTION91

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