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- PDB-4jga: X-ray crystal structure of 3-oxoacyl-[acyl-carrier-protein] synth... -

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Basic information

Entry
Database: PDB / ID: 4jga
TitleX-ray crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase 2 from Rickettsia rickettsii
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Synthase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity => GO:0004315 / beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesRickettsia rickettsii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: X-ray crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase 2 from Rickettsia rickettsii
Authors: Fairman, J.W. / Abendroth, J.A. / Edwards, T.E. / Lorimer, D.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5236
Polymers93,3602
Non-polymers1634
Water10,827601
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-47 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.170, 62.740, 95.430
Angle α, β, γ (deg.)90.000, 112.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 7 - 428 / Label seq-ID: 15 - 436

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THE THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 46680.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (bacteria) / Strain: Sheila Smith / Gene: A1G_06510 / Production host: Escherichia coli (E. coli)
References: UniProt: A8GTN0, UniProt: A0A0H3AY56*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 601 / 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: 43.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+ A10: 200 mM potassium formate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 47095 / Num. obs: 46577 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.917 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.2985.86165313194192
2.15-2.210.2757.41214883317199.1
2.21-2.280.2657.89214753241199.1
2.28-2.350.258.38214293178199.3
2.35-2.420.2348.92209573075199.5
2.42-2.510.219.89205462984199.6
2.51-2.60.18511.21200072892199.3
2.6-2.710.16112.76192302763199.8
2.71-2.830.14613.951857326431100
2.83-2.970.12716.09180792553199.6
2.97-3.130.11217.96173082421199.7
3.13-3.320.08423.77165692322199.9
3.32-3.550.06730152932155199.8
3.55-3.830.05138.131418220351100
3.83-4.20.0446.51129391850199.8
4.2-4.70.03652.56115811682199.6
4.7-5.420.04442.82105071497199.9
5.42-6.640.05534.9488711266199.7
6.64-9.390.03453.2668261002199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KZU

3kzu


Resolution: 2.1→19.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.982 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2355 5.1 %RANDOM
Rwork0.1479 ---
obs0.1494 46576 99.01 %-
all-47095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.2 Å2 / Biso mean: 15.695 Å2 / Biso min: 2.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.14 Å2
2--0.26 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 7 601 6813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196342
X-RAY DIFFRACTIONr_bond_other_d0.0040.026083
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9668614
X-RAY DIFFRACTIONr_angle_other_deg0.98314002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02624.723235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.598151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951525
X-RAY DIFFRACTIONr_chiral_restr0.0790.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217280
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021349
X-RAY DIFFRACTIONr_mcbond_it0.3670.6063384
X-RAY DIFFRACTIONr_mcbond_other0.3670.6063383
X-RAY DIFFRACTIONr_mcangle_it0.6460.9064229
Refine LS restraints NCS

Ens-ID: 1 / Number: 25770 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 158 -
Rwork0.188 3031 -
all-3189 -
obs--92.11 %
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)
11.15170.30130.29372.2461-0.18520.43590.0848-0.2569-0.1420.2952-0.0435-0.0770.01010.0871-0.04130.06440.0138-0.01670.15280.0160.0376-4.2593-13.5301-7.9045
22.1391.4984-1.12311.3048-0.98632.98980.2141-0.37810.08820.359-0.09760.0601-0.18050.2071-0.11660.20320.09550.00220.2027-0.02870.0388-12.29790.6166-2.6303
30.77480.3808-0.2861.121-0.17460.58370.0012-0.1152-0.08240.06240.0185-0.01650.04760.068-0.01970.03190.0054-0.01470.0490.01150.0198-18.0691-8.3818-12.4346
40.8645-0.05440.16370.6730.12461.05530.0114-0.0154-0.1252-0.04830.0066-0.17150.07830.2236-0.0180.03150.0210.00440.08080.00440.07380.036-13.5599-23.4182
55.63170.1551.28040.72390.28931.4789-0.04580.1275-0.0899-0.07230.1043-0.209-0.07440.2739-0.05860.06430.00040.00430.101-0.02660.06651.8281-8.2638-24.4681
61.65790.4995-1.29790.9807-0.68822.4914-0.02480.0012-0.1006-0.01420.01290.16770.1273-0.24070.01190.0292-0.0023-0.00520.05730.00180.0583-41.741-5.1298-26.2784
74.8144-0.66992.68942.8350.45997.10180.12570.1137-0.644-0.1505-0.18390.37750.5175-0.26340.05830.1056-0.044-0.0180.0625-0.01360.1809-35.9823-20.5454-30.2463
80.802-0.0573-0.29540.6448-0.0071.01210.005-0.0502-0.070.00230.00510.06290.0293-0.0242-0.01010.0146-0.0044-0.01350.00570.00840.0235-29.0852-7.9153-25.9575
91.21580.28950.05450.80590.08131.06660.0158-0.0440.19430.03140.00770.1441-0.1921-0.1617-0.02350.06240.02980.01630.02690.0040.0658-35.634411.7785-24.058
101.6539-0.33320.51231.5172-0.58274.0792-0.0304-0.01650.0261-0.0070.11760.1898-0.2945-0.4077-0.08720.06170.01130.02680.05120.0060.0753-32.610611.1046-30.4853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 59
2X-RAY DIFFRACTION2A60 - 111
3X-RAY DIFFRACTION3A112 - 232
4X-RAY DIFFRACTION4A233 - 399
5X-RAY DIFFRACTION5A400 - 427
6X-RAY DIFFRACTION6B7 - 59
7X-RAY DIFFRACTION7B60 - 86
8X-RAY DIFFRACTION8B87 - 266
9X-RAY DIFFRACTION9B267 - 399
10X-RAY DIFFRACTION10B400 - 428

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