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- PDB-3r1x: Crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsie... -

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Basic information

Entry
Database: PDB / ID: 3r1x
TitleCrystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae
Components2-oxo-3-deoxygalactonate kinase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / 2-oxo-3-deoxygalactonate kinase / 2-dehydro-3-deoxygalactonokinase / 2-keto-3-deoxygalactonate kinase / DeLey-Doudoroff pathway
Function / homology
Function and homology information


2-dehydro-3-deoxygalactonokinase activity / D-galactonate catabolic process
Similarity search - Function
2-keto-3-deoxy-galactonokinase, substrate binding domain / 2-keto-3-deoxy-galactonokinase, C-terminal domain / 2-keto-3-deoxy-galactonokinase / 2-keto-3-deoxy-galactonokinase, C-terminal domain / 2-keto-3-deoxy-galactonokinase, N-terminal / 2-keto-3-deoxy-galactonokinase / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 2-oxo-3-deoxygalactonate kinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.093 Å
AuthorsMichalska, K. / Cuff, M.E. / Tesar, C. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.
Authors: Michalska, K. / Cuff, M.E. / Tesar, C. / Feldmann, B. / Joachimiak, A.
History
DepositionMar 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
SupersessionJun 15, 2011ID: 3NUW
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 21, 2011Group: Other
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: 2-oxo-3-deoxygalactonate kinase
B: 2-oxo-3-deoxygalactonate kinase
C: 2-oxo-3-deoxygalactonate kinase
D: 2-oxo-3-deoxygalactonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,44225
Polymers126,6924
Non-polymers1,75021
Water9,728540
1
A: 2-oxo-3-deoxygalactonate kinase
B: 2-oxo-3-deoxygalactonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,35914
Polymers63,3462
Non-polymers1,01312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-30 kcal/mol
Surface area23490 Å2
MethodPISA
2
C: 2-oxo-3-deoxygalactonate kinase
D: 2-oxo-3-deoxygalactonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,08311
Polymers63,3462
Non-polymers7379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-31 kcal/mol
Surface area23300 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16060 Å2
ΔGint-67 kcal/mol
Surface area42720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.509, 134.026, 139.906
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
2-oxo-3-deoxygalactonate kinase


Mass: 31673.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: dgoK, KPN78578_40560, KPN_04097 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, pRK1037
References: UniProt: A6TFZ6, 2-dehydro-3-deoxygalactonokinase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M magnesium formate, 15%(w/v) PEG3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792064 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 5, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792064 Å / Relative weight: 1
ReflectionResolution: 2.093→50 Å / Num. all: 95105 / Num. obs: 94834 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.5
Reflection shellResolution: 2.093→2.14 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4700 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.093→35.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.316 / SU ML: 0.099 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19915 1902 2 %RANDOM
Rwork0.17398 ---
all0.17448 94473 --
obs0.17448 94473 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.093→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8795 0 114 540 9449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0219438
X-RAY DIFFRACTIONr_bond_other_d0.0020.026285
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.95412863
X-RAY DIFFRACTIONr_angle_other_deg0.95315255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12451237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21123.079406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.758151448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8481586
X-RAY DIFFRACTIONr_chiral_restr0.0930.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021958
X-RAY DIFFRACTIONr_mcbond_it0.6471.56026
X-RAY DIFFRACTIONr_mcbond_other0.1791.52479
X-RAY DIFFRACTIONr_mcangle_it1.1729638
X-RAY DIFFRACTIONr_scbond_it2.10233412
X-RAY DIFFRACTIONr_scangle_it3.2524.53221
LS refinement shellResolution: 2.093→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 166 -
Rwork0.234 6482 -
obs-6482 95.61 %
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)
11.574-0.00420.3036.17541.93264.40380.0538-0.064-0.16530.2523-0.0901-0.16050.037-0.07150.03630.0832-0.0193-0.02670.09660.0290.137166.8041121.340534.6966
21.23531.15261.109211.09043.84426.0511-0.0457-0.2028-0.14010.39820.0934-0.51850.00260.4069-0.04770.198-0.0482-0.06690.19910.03660.225674.2954128.373141.4875
33.3263-0.1492.49522.2287-1.0484.8360.05160.17140.0766-0.1897-0.1501-0.2609-0.28270.18430.09850.0987-0.01540.06520.0873-0.00450.111267.6432134.569324.9509
47.3485-4.19331.0465.7978-0.84381.56040.04950.18590.141-0.1356-0.1538-0.3469-0.08080.11980.10430.111-0.02560.04370.0751-0.02360.053464.1478136.551122.8985
51.4072-0.7393-1.05141.46480.68461.2832-0.0292-0.0586-0.19360.033-0.03110.2410.0522-0.00740.06030.1065-0.0128-0.00260.1042-0.01330.135140.9235136.881232.6631
68.2913-2.58340.42473.26950.39370.77840.06650.3388-0.1581-0.1998-0.19320.4040.0764-0.12010.12670.1805-0.0360.00680.1198-0.04970.141148.8374125.676324.3955
71.5376-1.67140.95888.4279-1.20863.83310.0209-0.01950.05450.1156-0.0645-0.2542-0.09230.17960.04350.1283-0.01790.03450.14320.03940.076831.8666173.55957.3656
82.221-3.3547-1.38958.52412.46293.5673-0.1549-0.2827-0.04260.49220.202-0.35320.10560.207-0.04710.21650.01690.00050.24080.07010.120133.4874165.988966.5175
92.3371.31361.90383.73073.56364.99860.0639-0.0718-0.3970.2903-0.12670.23920.4926-0.23550.06280.1524-0.00190.08480.13590.06390.194824.0498158.249955.0314
101.10210.0595-0.52482.77140.10892.47990.0445-0.0434-0.2130.1456-0.04990.2553-0.0207-0.21140.00540.08240.01490.03570.12910.00860.209421.9627161.366145.9709
113.9294-0.4511-0.88281.35530.25380.79710.0644-0.03740.1087-0.0678-0.04280.016-0.14490.0455-0.02160.13020.0160.00510.0682-0.00370.05843.4827155.757132.316
122.9291-1.7295-3.06212.25961.99535.77130.19080.24880.0827-0.3168-0.17950.108-0.2087-0.1988-0.01130.15760.0340.00120.09410.0340.139230.6656168.614736.6121
1324.90012.9709-1.48373.1312-9.093128.78220.4871-1.9337-2.0653-0.68870.3590.09922.5057-1.3221-0.84610.8677-0.1372-0.02850.39270.21690.664153.3451112.677660.9175
143.767-1.3380.06757.4631.10833.9020.11740.0334-0.5161-0.1927-0.26240.40810.4929-0.39360.1450.2486-0.0272-0.00080.25960.00020.273750.625123.798250.4423
152.98380.61540.2392.04670.30081.59880.0372-0.1864-0.29690.3012-0.07420.08960.2904-0.22260.0370.2839-0.02320.01520.30980.07780.125257.8884134.70265.3703
162.10630.631-1.31231.52680.13832.2297-0.0906-0.0672-0.1717-0.00930.1281-0.32270.10450.1312-0.03750.08380.0235-0.03020.1687-0.02340.184576.3648146.073550.6053
172.4404-0.46483.47350.42531.24715.8450.0455-0.20550.39540.1140.1861-0.24620.46760.3139-0.23160.57510.0055-0.15470.50430.11170.359374.4626136.982370.3787
189.95235.63630.15146.0879-0.05921.0550.2074-0.4797-0.27960.4424-0.1394-0.21510.41220.1441-0.0680.34420.0937-0.03160.26850.1170.231369.5475128.465760.9865
194.2841-0.1953-0.14087.50280.54663.9374-0.06760.66690.4217-1.18010.06940.5785-0.5859-0.4505-0.00180.5718-0.0914-0.02390.46030.06750.286471.8888175.206825.3282
202.12760.3661-0.6984.7845-2.43544.484-0.07110.26040.176-0.3472-0.0073-0.4055-0.21140.37650.07840.2118-0.11890.09740.2711-0.09050.288785.7948169.015636.9148
212.45791.697-0.26073.5665-0.15651.356-0.11160.16260.2258-0.23530.2693-0.289-0.36220.1308-0.15770.1792-0.05950.04620.2133-0.05020.195577.7718169.382848.0636
225.68170.26022.12583.2810.52013.18780.05330.009-0.0573-0.04570.11510.17020.1548-0.4354-0.16840.12250.01080.06610.29120.04640.119158.8252158.273756.236
235.65571.0951-1.31013.7869-0.55322.08260.0575-0.05340.04030.16790.08810.18110.0025-0.2741-0.14570.11140.0261-0.00870.23530.00390.020661.2566155.849857.8035
241.35441.3978-2.18912.7772-3.00717.2987-0.0086-0.08030.29430.14450.0227-0.1487-0.6240.2336-0.01410.3138-0.00530.04760.1992-0.03870.3273.6992176.346149.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 36
2X-RAY DIFFRACTION2A37 - 56
3X-RAY DIFFRACTION3A57 - 87
4X-RAY DIFFRACTION4A88 - 121
5X-RAY DIFFRACTION5A122 - 238
6X-RAY DIFFRACTION6A239 - 292
7X-RAY DIFFRACTION7B1 - 32
8X-RAY DIFFRACTION8B33 - 58
9X-RAY DIFFRACTION9B59 - 82
10X-RAY DIFFRACTION10B83 - 135
11X-RAY DIFFRACTION11B136 - 238
12X-RAY DIFFRACTION12B239 - 292
13X-RAY DIFFRACTION13C1 - 5
14X-RAY DIFFRACTION14C6 - 75
15X-RAY DIFFRACTION15C76 - 148
16X-RAY DIFFRACTION16C149 - 238
17X-RAY DIFFRACTION17C239 - 249
18X-RAY DIFFRACTION18C250 - 292
19X-RAY DIFFRACTION19D1 - 75
20X-RAY DIFFRACTION20D76 - 121
21X-RAY DIFFRACTION21D122 - 168
22X-RAY DIFFRACTION22D169 - 198
23X-RAY DIFFRACTION23D199 - 239
24X-RAY DIFFRACTION24D240 - 292

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