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

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Basic information

Entry
Database: PDB / ID: 4ijk
TitleCrystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Helicobacter pylori 26695
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
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsHou, J. / Osinski, T. / Zheng, H. / Shumilin, I. / Shabalin, I.G. / 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
Authors: Hou, J. / Osinski, T. / Zheng, H. / Shumilin, I. / Shabalin, I.G. / Shatsman, S. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 21, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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)117,7975
Polymers117,7744
Non-polymers231
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-99 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.168, 114.642, 69.501
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYRAA1 - 24625 - 270
21METMETTYRTYRBB1 - 24625 - 270
12METMETMETMETAA1 - 24725 - 271
22METMETMETMETCC1 - 24725 - 271
13ALAALATYRTYRAA0 - 24624 - 270
23ALAALATYRTYRDD0 - 24624 - 270
14METMETTYRTYRBB1 - 24625 - 270
24METMETTYRTYRCC1 - 24625 - 270
15METMETTYRTYRBB1 - 24625 - 270
25METMETTYRTYRDD1 - 24625 - 270
16METMETTYRTYRCC1 - 24625 - 270
26METMETTYRTYRDD1 - 24625 - 270

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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M sodium fluoride, 22.5% 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: 2.54→50 Å / Num. obs: 33838 / % possible obs: 98.9 % / Redundancy: 5 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.4
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1632 / % possible all: 97.2

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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 reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OSU

3osu


Resolution: 2.54→46.96 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.844 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 21.697 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.056 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 1606 5.1 %RANDOM
Rwork0.2347 ---
obs0.2366 31612 92.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.8 Å2 / Biso mean: 27.2763 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0 Å20 Å2
2--3.02 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.54→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 1 94 6882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196888
X-RAY DIFFRACTIONr_bond_other_d0.0070.026648
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9519283
X-RAY DIFFRACTIONr_angle_other_deg1.184315206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45324.943261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0091526
X-RAY DIFFRACTIONr_chiral_restr0.070.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027933
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021529
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126450.08
12B126450.08
21A133120.07
22C133120.07
31A125940.07
32D125940.07
41B127770.09
42C127770.09
51B125590.08
52D125590.08
61C127490.09
62D127490.09
LS refinement shellResolution: 2.54→2.608 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 70 -
Rwork0.26 1337 -
all-1407 -
obs--57.26 %
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)
13.08031.7597-3.51112.4864-0.05769.19150.0747-0.18930.19940.18070.1198-0.0454-0.00130.6124-0.19450.0980.0215-0.05550.0529-0.04720.2025-10.96122.714-3.692
20.65210.026-0.21010.07230.15390.72040.0101-0.05110.0875-0.020.0385-0.02560.15140.1725-0.04860.17850.0324-0.02460.0416-0.0160.1879-10.83615.308-14.378
30.2565-0.2408-0.02092.8912-0.64480.91320.08380.0161-0.021-0.06160.09730.09650.00930.044-0.18110.1702-0.0147-0.0060.0168-0.00950.1487-22.1925.387-11.533
41.1818-0.57050.15081.4230.28540.3553-0.0648-0.06470.0503-0.11910.0290.12170.12130.07610.03590.25470.0513-0.01550.043-0.03050.1223-32.6745.539-46.769
50.3485-0.35551.3971.7042-3.14768.25950.1150.0565-0.0186-0.07170.03160.01720.58410.0064-0.14670.25030.0026-0.02730.04370.00210.1521-21.9496.132-29.209
60.2697-0.11510.21091.1097-0.19660.1785-0.01320.0518-0.02190.02510.03130.0534-0.03760.0336-0.01810.21190.0113-0.00180.0136-0.00840.1539-35.22315.984-33.057
70.63420.06870.45370.0596-0.09021.2146-0.0334-0.04390.0535-0.0411-0.02180.0735-0.0656-0.01640.05520.16760.0352-0.03850.0112-0.02470.2161-57.51635.233-30.993
80.0056-0.0167-0.02070.8444-0.06010.16550.01760.00610.00470.0497-0.01250.1399-0.0434-0.0188-0.00510.1723-0.0008-0.01570.0345-0.0170.1845-46.78529.152-25.225
91.0587-0.0863-0.6910.9949-0.34410.68-0.01930.0085-0.0689-0.12760.0073-0.0465-0.0262-0.00910.0120.23930.0079-0.02350.0012-0.01170.1471-40.69327.225-34.913
101.3331-0.76340.56261.32821.03793.29030.04-0.1374-0.0880.1797-0.00370.12070.0972-0.0544-0.03640.2421-0.01310.04950.06080.02730.133-34.44738.1479.856
110.68970.19330.46260.07370.20860.8803-0.078-0.0479-0.0072-0.0153-0.010.0108-0.08-0.10560.08810.1964-0.00120.01650.0313-0.0050.1653-41.07738.282-6.125
121.81630.6538-1.14532.2392-0.78880.8556-0.0345-0.07740.01240.10280.14490.1508-0.06260.0243-0.11040.2115-0.0206-0.02820.02330.02140.1863-30.6425.571-3.404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 29
2X-RAY DIFFRACTION2A30 - 164
3X-RAY DIFFRACTION3A165 - 247
4X-RAY DIFFRACTION4B1 - 90
5X-RAY DIFFRACTION5B91 - 129
6X-RAY DIFFRACTION6B130 - 246
7X-RAY DIFFRACTION7C1 - 130
8X-RAY DIFFRACTION8C131 - 205
9X-RAY DIFFRACTION9C206 - 247
10X-RAY DIFFRACTION10D0 - 58
11X-RAY DIFFRACTION11D59 - 207
12X-RAY DIFFRACTION12D208 - 246

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