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- PDB-4iiv: Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]r... -

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Basic information

Entry
Database: PDB / ID: 4iiv
TitleCrystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.5 A resolution
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / short chain dehydrogenase / FabG / beta-ketoacyl-acyl carrier protein reductase / Rossmann fold
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase, putative / : / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier protein] reductase / 3-oxoacyl-[acyl-carrier protein] reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHou, J. / Osinski, T. / Zheng, H. / Shumilin, I. / Shabalin, I. / Shatsman, S. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.5 A resolution
Authors: Hou, J. / Osinski, T. / Zheng, H. / Shumilin, I. / Shabalin, I. / Shatsman, S. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8198
Polymers113,8464
Non-polymers2,9744
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17390 Å2
ΔGint-95 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.477, 127.477, 122.951
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 243 / Label seq-ID: 26 - 267

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 28461.430 Da / Num. of mol.: 4 / Mutation: C20R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: c1187, NT04EC1225 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q8FJ14, UniProt: A0A0H2V833*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 8.5, 27.5% w/v PEG3350, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2012 / Details: MIRRORS
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 39057 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1943 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OSU

3osu


Resolution: 2.5→41.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.1971 / WRfactor Rwork: 0.1628 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8566 / SU B: 8.067 / SU ML: 0.177 / SU R Cruickshank DPI: 0.5287 / SU Rfree: 0.2588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.529 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1899 5 %RANDOM
Rwork0.1804 ---
obs0.1824 37974 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.2 Å2 / Biso mean: 35.2639 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.3 Å20 Å2
2---0.3 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 192 299 7514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197376
X-RAY DIFFRACTIONr_bond_other_d0.0050.027051
X-RAY DIFFRACTIONr_angle_refined_deg1.511.97810017
X-RAY DIFFRACTIONr_angle_other_deg1.129316069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97123.677291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.652151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2571558
X-RAY DIFFRACTIONr_chiral_restr0.0710.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028541
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021717
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A136760.09
12B136760.09
21A142630.07
22C142630.07
31A142950.07
32D142950.07
41B137390.07
42C137390.07
51B135390.09
52D135390.09
61C139740.07
62D139740.07
LS refinement shellResolution: 2.5→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 86 -
Rwork0.217 1972 -
all-2058 -
obs--71.78 %

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