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- PDB-3khy: Crystal Structure of a propionate kinase from Francisella tularen... -

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Basic information

Entry
Database: PDB / ID: 3khy
TitleCrystal Structure of a propionate kinase from Francisella tularensis subsp. tularensis SCHU S4
ComponentsPropionate kinase
KeywordsTRANSFERASE / propionate kinase / CSGID / IDP01739 / ATP-binding / Kinase / Nucleotide-binding / Structural Genomics / National Institute of Allergy and Infectious Diseases / National Institutes of Health / Department of Health and Human Services / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.978 Å
AuthorsBrunzelle, J.S. / Skarina, T. / Sharma, S. / Wang, Y. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of a propionate kinase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Brunzelle, J.S. / Sharma, S.S. / Skarina, T. / Wang, Y. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 1, 2014Group: Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propionate kinase
B: Propionate kinase


Theoretical massNumber of molelcules
Total (without water)85,5192
Polymers85,5192
Non-polymers00
Water11,818656
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-50 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.079, 87.127, 149.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Propionate kinase


Mass: 42759.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: FTT1753, FTT_1753, tdcD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q5NE95, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a carboxy group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NaFormate 4M, 0.3M 195 NDSB, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 23, 2009 / Details: Be-Lenes
RadiationMonochromator: Diamond-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 117233 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 18
Reflection shellResolution: 1.97→2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.7 / Num. unique all: 5848 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIX(phenix.AutoSol: 1.4_115)model building
PHENIX(phenix.refine: 1.4_115)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.4_115phasing
RefinementMethod to determine structure: SAD / Resolution: 1.978→28.51 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 3066 5.08 %RANDOM
Rwork0.1553 ---
all0.1572 60374 --
obs0.1553 60374 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.227 Å2 / ksol: 0.37 e/Å3
Refinement stepCycle: LAST / Resolution: 1.978→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5923 0 0 656 6579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076080
X-RAY DIFFRACTIONf_angle_d1.0118225
X-RAY DIFFRACTIONf_dihedral_angle_d16.7642191
X-RAY DIFFRACTIONf_chiral_restr0.071953
X-RAY DIFFRACTIONf_plane_restr0.0041051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.978-2.0490.24172920.16394974X-RAY DIFFRACTION86
2.049-2.1310.19612900.14825598X-RAY DIFFRACTION96
2.131-2.2280.20272980.14365654X-RAY DIFFRACTION97
2.228-2.34540.19182990.1415724X-RAY DIFFRACTION98
2.3454-2.49230.20263110.14925750X-RAY DIFFRACTION98
2.4923-2.68460.20983130.16155766X-RAY DIFFRACTION99
2.6846-2.95450.21752970.18275852X-RAY DIFFRACTION100
2.9545-3.38140.21253170.17215883X-RAY DIFFRACTION100
3.3814-4.25790.16473280.13435937X-RAY DIFFRACTION100
4.2579-28.51340.1693210.15336170X-RAY DIFFRACTION100
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)
10.1045-0.09670.02620.5675-0.05760.9269-0.2171-0.07380.1013-0.15730.0157-0.08050.5254-0.0736-0.00550.3343-0.07190.05550.2106-0.0230.154340.720733.201367.8238
20.4807-0.0187-0.17590.6809-0.17170.5184-0.2282-0.072-0.1876-0.09780.1159-0.15430.71370.18720.01330.34570.12210.06980.211-0.01610.180945.589231.478476.845
30.13890.0920.04550.32250.17080.8149-0.2637-0.0755-0.33130.0009-0.02330.00980.8473-0.1576-0.00180.61750.03720.10050.15430.00820.270139.26826.75185.3165
40.3123-0.2913-0.18790.3704-0.24330.9780.0053-0.04570.00290.0186-0.0021-0.0420.15940.23690.00540.11480.0237-0.02190.12660.01280.115536.051847.707291.0271
50.774-0.1778-0.45890.3679-0.22360.5333-0.04440.1505-0.0882-0.0589-0.0339-0.020.1743-0.1236-0.00020.1191-0.020.00190.1553-0.01340.127115.573148.046479.4866
60.4646-0.0775-0.18390.17590.01660.90820.05180.02460.08690.02590.021-0.072-0.07860.107-00.0805-0.01110.00210.13450.00560.124835.573760.379680.5116
70.70460.19410.51930.5625-0.19321.66050.2619-0.1029-0.04440.1165-0.11480.2073-0.0609-0.0087-0.00090.1927-00.03330.10330.00630.178-7.00458.1992119.4931
80.86340.2285-0.24490.7678-0.30680.8336-0.02220.3246-0.1535-0.0074-0.04720.09650.0361-0.4055-0.12020.07810.01320.01360.2324-0.02590.1567-8.578156.4183101.3174
90.39240.0433-0.20110.40030.36290.5060.06670.01930.04420.0128-0.0110.109-0.0397-0.17660.01010.09890.00730.01010.10470.01450.12189.363262.672394.2102
100.55810.189-0.25250.36690.04230.2066-0.0518-0.1513-0.08710.1447-0.03660.1190.0441-0.0241-0.01060.1706-0.00020.01360.12960.03330.120819.638446.03106.1427
110.5819-0.05-0.03350.64520.51940.45620.0483-0.16630.18940.09080.0378-0.1422-0.13440.1604-00.1194-0.01950.00680.1237-0.03810.136923.304769.5328105.1893
120.46360.0037-0.49490.15960.12180.62510.3209-0.00210.2421-0.3385-0.1798-0.1031-0.48780.05570.040.28720.06250.07340.11820.04910.2288-4.177969.139105.5052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:61)A1 - 61
2X-RAY DIFFRACTION2(chain A and resid 62:99)A62 - 99
3X-RAY DIFFRACTION3(chain A and resid 100:134)A100 - 134
4X-RAY DIFFRACTION4(chain A and resid 135:224)A135 - 224
5X-RAY DIFFRACTION5(chain A and resid 225:298)A225 - 298
6X-RAY DIFFRACTION6(chain A and resid 299:384)A299 - 384
7X-RAY DIFFRACTION7(chain B and resid 1:77)B1 - 77
8X-RAY DIFFRACTION8(chain B and resid 78:141)B78 - 141
9X-RAY DIFFRACTION9(chain B and resid 142:224)B142 - 224
10X-RAY DIFFRACTION10(chain B and resid 225:299)B225 - 299
11X-RAY DIFFRACTION11(chain B and resid 300:370)B300 - 370
12X-RAY DIFFRACTION12(chain B and resid 371:384)B371 - 384

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