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- PDB-3rro: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -

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Basic information

Entry
Database: PDB / ID: 3rro
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) from Vibrio cholerae
Components3-ketoacyl-(acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / FabG / acyl carrier protein / Cell Plasma
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / 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-oxoacyl-(acyl-carrier-protein) reductase / : / 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
TRIETHYLENE GLYCOL / : / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHou, J. / Chruszcz, M. / Cooper, D.R. / Grabowski, M. / Zheng, H. / Osinski, T. / Shumilin, I. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Bacteriol. / Year: 2015
Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.
Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Mar 23, 2016Group: Database references
Revision 1.4Apr 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 1.5Sep 13, 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-ketoacyl-(acyl-carrier-protein) reductase
B: 3-ketoacyl-(acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,73125
Polymers52,7162
Non-polymers2,01523
Water3,567198
1
A: 3-ketoacyl-(acyl-carrier-protein) reductase
B: 3-ketoacyl-(acyl-carrier-protein) reductase
hetero molecules

A: 3-ketoacyl-(acyl-carrier-protein) reductase
B: 3-ketoacyl-(acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,46350
Polymers105,4324
Non-polymers4,03046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area22890 Å2
ΔGint-288 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.939, 63.939, 190.146
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-255-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU2AA2 - 1895 - 192
21SERSERGLUGLU2BB2 - 1895 - 192
12THRTHRALAALA4AA190 - 210193 - 213
22THRTHRALAALA4BB190 - 210193 - 213
13GLYGLYILEILE2AA211 - 248214 - 251
23GLYGLYILEILE2BB211 - 248214 - 251

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 26358.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VCD_002346 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus
References: UniProt: C3NP04, UniProt: Q9KQH7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase

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Non-polymers , 6 types, 221 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris pH9, 5% Tacsimate, 2.6M Ammonium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, 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 315r / Detector: CCD / Date: Mar 18, 2011 / 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.644
11-H-K, K, -L20.356
ReflectionResolution: 2→25 Å / Num. all: 29605 / Num. obs: 29605 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1455 / Rsym value: 0.404 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP4

3op4


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.509 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17922 1430 5 %RANDOM
Rwork0.13885 ---
all0.14091 27004 --
obs0.14091 27004 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.23 Å2
Baniso -1Baniso -2Baniso -3
1--6.23 Å20 Å20 Å2
2---6.23 Å20 Å2
3---12.46 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 115 198 3920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223760
X-RAY DIFFRACTIONr_bond_other_d0.0070.022500
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9875061
X-RAY DIFFRACTIONr_angle_other_deg2.42336118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78324.685143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0115643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5071526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024179
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02697
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6021.52439
X-RAY DIFFRACTIONr_mcbond_other0.0841.51037
X-RAY DIFFRACTIONr_mcangle_it0.99523879
X-RAY DIFFRACTIONr_scbond_it1.84331321
X-RAY DIFFRACTIONr_scangle_it2.9314.51181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11106TIGHT POSITIONAL0.030.05
11191MEDIUM POSITIONAL0.060.5
11106TIGHT THERMAL0.120.5
11191MEDIUM THERMAL0.122
2241MEDIUM POSITIONAL0.230.5
2241MEDIUM THERMAL0.162
3221TIGHT POSITIONAL0.080.05
3244MEDIUM POSITIONAL0.360.5
3221TIGHT THERMAL0.430.5
3244MEDIUM THERMAL0.572
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 74 -
Rwork0.145 1241 -
obs--60.54 %
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)
14.4383-0.60590.75462.157-0.15172.85890.39740.56390.0172-0.235-0.3494-0.2866-0.07570.3344-0.0480.31920.17450.08020.34090.05360.0965-7.261-11.327-17.507
21.9776-0.374-0.30671.6183-0.09261.20230.31770.3143-0.0852-0.4594-0.2198-0.1270.05030.0932-0.09790.30050.13140.01770.22560.00650.0323-23.249-5.848-18.139
32.5503-0.4476-0.13022.04820.88631.21310.2745-0.06080.3193-0.3804-0.1752-0.2885-0.20410.156-0.09930.20280.00550.07630.19350.0430.0689-15.11.635-4.574
43.0812-0.7951-0.96762.7725-0.32684.6189-0.069-0.6882-0.1880.19530.0299-0.16630.06950.27250.0390.1063-0.0313-0.04480.59930.150.0688-10.306-13.59619.411
52.4808-0.3627-0.20080.9461-0.45760.74610.1001-0.8295-0.07870.0717-0.0276-0.0141-0.00770.0475-0.07250.1186-0.0721-0.01250.51670.05230.0307-23.76-5.04516.521
62.38-0.110.24981.85960.08341.47050.1899-0.3328-0.3961-0.023-0.11480.1190.2085-0.0468-0.07510.1315-0.0247-0.03630.23090.08480.0787-24.744-14.9083.736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 192
3X-RAY DIFFRACTION3A193 - 248
4X-RAY DIFFRACTION4B2 - 78
5X-RAY DIFFRACTION5B79 - 195
6X-RAY DIFFRACTION6B196 - 248

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