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

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Basic information

Entry
Database: PDB / ID: 4iin
TitleCrystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Helicobacter pylori 26695 complexed with NAD+
Components3-ketoacyl-acyl carrier protein reductase (FabG)
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 / fatty acid biosynthetic process / NAD 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-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 Helicobacter pylori 26695 complexed with NAD+
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-ketoacyl-acyl carrier protein reductase (FabG)
B: 3-ketoacyl-acyl carrier protein reductase (FabG)
C: 3-ketoacyl-acyl carrier protein reductase (FabG)
D: 3-ketoacyl-acyl carrier protein reductase (FabG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,68313
Polymers117,7744
Non-polymers2,9099
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18110 Å2
ΔGint-106 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.923, 112.094, 70.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 0 - 247 / Label seq-ID: 24 - 271

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-ketoacyl-acyl carrier protein reductase (FabG)


Mass: 29443.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP0561, HP_0561 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: O25286, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M potassium acetate, 25% 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: 2.4→50 Å / Num. obs: 40094 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.2

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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: 2.4→43.87 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.859 / WRfactor Rfree: 0.2467 / WRfactor Rwork: 0.2128 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8414 / SU B: 8.099 / SU ML: 0.191 / SU R Cruickshank DPI: 0.5546 / SU Rfree: 0.2861 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 1918 5 %RANDOM
Rwork0.2166 ---
obs0.2185 38168 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.05 Å2 / Biso mean: 23.5555 Å2 / Biso min: 2.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0 Å2
2--0.19 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6963 0 190 168 7321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197252
X-RAY DIFFRACTIONr_bond_other_d0.0070.026905
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9859806
X-RAY DIFFRACTIONr_angle_other_deg1.194315806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62524.706272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.504151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.151530
X-RAY DIFFRACTIONr_chiral_restr0.0790.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028236
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021630
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A135860.07
12B135860.07
21A136770.07
22C136770.07
31A134900.08
32D134900.08
41B136320.07
42C136320.07
51B134800.08
52D134800.08
61C136250.07
62D136250.07
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 75 -
Rwork0.245 1759 -
all-1834 -
obs--61.75 %

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