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

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Basic information

Entry
Database: PDB / ID: 4iiu
TitleCrystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.1 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
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: 2.1 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 2.1 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
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17330 Å2
ΔGint-98 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.541, 128.541, 125.938
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 / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA2 - 24226 - 266
21METMETBB2 - 24226 - 266
12LEULEUAA2 - 24326 - 267
22LEULEUCC2 - 24326 - 267
13METMETAA2 - 24226 - 266
23METMETDD2 - 24226 - 266
14LEULEUBB2 - 24326 - 267
24LEULEUCC2 - 24326 - 267
15LEULEUBB2 - 24326 - 267
25LEULEUDD2 - 24326 - 267
16LEULEUCC2 - 24326 - 267
26LEULEUDD2 - 24326 - 267

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.: 495 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2012 / Details: MIRRORS
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 68701 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 45.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3403 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3osu


Resolution: 2.1→39.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.852 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 3427 5.1 %RANDOM
Rwork0.1679 ---
obs0.1692 67856 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.95 Å2 / Biso mean: 34.3943 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.43 Å2-0 Å2
2---0.43 Å2-0 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7016 0 192 495 7703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197384
X-RAY DIFFRACTIONr_bond_other_d0.0040.027073
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.97810031
X-RAY DIFFRACTIONr_angle_other_deg1.03316109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3965974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5223.544285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.193151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.551558
X-RAY DIFFRACTIONr_chiral_restr0.0720.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028548
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021718
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137420.08
12B137420.08
21A137900.08
22C137900.08
31A140200.08
32D140200.08
41B139820.07
42C139820.07
51B139680.08
52D139680.08
61C138330.08
62D138330.08
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 224 -
Rwork0.21 3993 -
all-4217 -
obs--83.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9802-0.022-0.32282.54170.27761.85330.18330.39920.3469-0.2337-0.2307-0.2362-0.24210.05810.04740.10190.07530.05980.19760.11440.088643.78668.762-7.866
21.78150.2446-0.46160.8346-0.02330.7888-0.04230.2982-0.1115-0.0929-0.0751-0.07850.1071-0.00380.11740.11620.05430.04580.1994-0.01850.037938.15952.909-5.169
33.2523-1.27140.60471.41940.06782.0490.2050.38870.0525-0.2008-0.27650.0281-0.117-0.20010.07150.11680.0930.02930.20380.00680.0226.25765.017-0.773
41.6083-0.0171-0.68261.9423-0.12831.2424-0.1856-0.0337-0.31020.3867-0.1990.35820.3298-0.54930.38460.3243-0.22740.25860.4587-0.15740.2757-1.43345.76324.826
52.0415-0.0537-0.84681.95220.86750.8323-0.19680.1606-0.32940.2881-0.14410.22170.2628-0.3090.34090.2183-0.10890.16220.3386-0.17370.214710.05748.21717.925
61.6098-0.96250.36912.876-0.55373.5384-0.1590.3602-0.18560.0464-0.21220.19910.0729-0.71030.37120.1567-0.11670.13560.4256-0.20460.16365.19647.246.462
77.33547.9252-0.092914.2741-1.84486.1858-0.41580.38050.3718-0.42150.0740.44510.3203-0.34760.34190.467-0.27630.12710.468-0.35060.35049.91528.295-7.81
83.1524-0.506-1.27052.8325-0.09243.1394-0.36750.1901-0.95030.0975-0.14790.19580.8438-0.14460.51540.6432-0.30060.27460.4526-0.36620.536519.25223.114-6.209
91.3893-0.1384-0.31351.31620.47121.2791-0.16860.3121-0.40730.0233-0.12390.02390.4414-0.23640.29250.2352-0.08580.13730.22-0.15860.175721.67537.644-1.293
101.860.0125-0.04172.1505-0.08442.6593-0.0566-0.20850.2270.21720.0234-0.2487-0.11010.21630.03310.1320.0242-0.02160.0988-0.03910.063129.72677.36326.277
110.8135-0.0109-0.23171.55670.15720.8324-0.0164-0.05460.05960.1811-0.0480.0136-0.0461-0.14540.06440.14420.03760.02720.1386-0.02290.02417.10168.78523.607
122.2226-1.2601-0.16142.3084-0.06161.8705-0.1348-0.1891-0.03340.23450.0742-0.03940.0908-0.04970.06060.12560.02940.02350.10290.00970.010429.63362.16316.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 55
2X-RAY DIFFRACTION2A56 - 176
3X-RAY DIFFRACTION3A177 - 243
4X-RAY DIFFRACTION4B2 - 129
5X-RAY DIFFRACTION5B130 - 189
6X-RAY DIFFRACTION6B190 - 243
7X-RAY DIFFRACTION7C2 - 7
8X-RAY DIFFRACTION8C8 - 68
9X-RAY DIFFRACTION9C69 - 243
10X-RAY DIFFRACTION10D2 - 49
11X-RAY DIFFRACTION11D50 - 171
12X-RAY DIFFRACTION12D172 - 243

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