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- PDB-4eum: Crystal structure of a sugar kinase (Target EFI-502132) from Ocea... -

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Basic information

Entry
Database: PDB / ID: 4eum
TitleCrystal structure of a sugar kinase (Target EFI-502132) from Oceanicola granulosus with bound AMP, crystal form II
Components2-dehydro-3-deoxygluconokinase
KeywordsTRANSFERASE / putative sugar kinase / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance metabolic process / kinase activity / phosphorylation / nucleotide binding
Similarity search - Function
pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / KDG kinase
Similarity search - Component
Biological speciesOceanicola granulosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a sugar kinase (Target EFI-502132) from Oceanicola granulosus with bound AMP, crystal form II
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-dehydro-3-deoxygluconokinase
B: 2-dehydro-3-deoxygluconokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0879
Polymers69,2262
Non-polymers8617
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-61 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.540, 49.528, 83.267
Angle α, β, γ (deg.)90.000, 101.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-dehydro-3-deoxygluconokinase /


Mass: 34612.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanicola granulosus (bacteria) / Strain: HTCC2516 / Gene: OG2516_05533 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2CIP5, 2-dehydro-3-deoxygluconokinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 298 K / Method: sitting drop, vapor diffusion / pH: 4
Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM AMP-PNP), reservoir (0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350), cryoprotectant ...Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM AMP-PNP), reservoir (0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350), cryoprotectant (reservoir + 20% glycerol), SITTING DROP, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 19, 2012 / Details: MIRRORS
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→81.595 Å / Num. all: 56642 / Num. obs: 56642 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.08 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.20.6451.22641282430.64595.9
1.9-2.013.30.3552.12597778320.35596.8
2.01-2.153.40.2073.72548674720.20797.3
2.15-2.323.50.15152397468590.15197
2.32-2.553.60.1156.52269363810.11597.1
2.55-2.853.60.0937.82058657290.09396.5
2.85-3.293.60.0719.51806550540.07196.1
3.29-4.023.50.05711.61472841730.05793.3
4.02-5.693.60.04813.51168432760.04893.7
5.69-77.9433.40.03916.7544316230.03982.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LHX

3lhx


Resolution: 1.8→27.198 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8565 / SU ML: 0.27 / σ(F): 1.33 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2847 5.03 %RANDOM
Rwork0.1763 ---
obs0.1786 56598 95.46 %-
all-56598 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.176 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso max: 99.37 Å2 / Biso mean: 31.5299 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.6208 Å20 Å2-1.2618 Å2
2--4.3788 Å2-0 Å2
3----1.758 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 51 426 4897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074631
X-RAY DIFFRACTIONf_angle_d1.1096321
X-RAY DIFFRACTIONf_chiral_restr0.074708
X-RAY DIFFRACTIONf_plane_restr0.004836
X-RAY DIFFRACTIONf_dihedral_angle_d13.9031641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8310.39441490.32012685283496
1.831-1.86430.37881360.30522643277995
1.8643-1.90020.37861450.28262701284696
1.9002-1.9390.32441400.23512684282496
1.939-1.98110.27641410.20732725286697
1.9811-2.02720.22891310.18462678280997
2.0272-2.07790.20871080.17712756286497
2.0779-2.1340.21481420.17582713285597
2.134-2.19680.23241420.17782737287997
2.1968-2.26770.2341550.17262665282096
2.2677-2.34870.21221440.17182738288297
2.3487-2.44260.21681500.17142689283997
2.4426-2.55370.19281460.16452722286897
2.5537-2.68830.2091370.16942713285096
2.6883-2.85650.27611450.18052706285196
2.8565-3.07680.23921320.18152727285996
3.0768-3.38590.2061550.15782649280495
3.3859-3.87460.19291620.14742620278293
3.8746-4.8770.16621570.13682651280893
4.877-27.20150.22471300.20692549267987
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)
10.78910.55660.4841.5282.64034.9125-0.04630.2734-0.1107-0.2206-0.0180.122-0.2583-0.0870.06160.2250.0267-0.01130.2906-0.00090.1728-14.72455.9844120.8078
20.99150.0808-0.26450.5843-0.45111.5508-0.08890.003-0.0205-0.28230.0411-0.01090.18050.08450.04930.2294-0.0188-0.01190.1373-0.00720.1761-3.784444.700399.2008
31.52610.1208-0.06621.43650.41462.121-0.0150.19120.1721-0.1188-0.04880.2196-0.2817-0.20530.03910.16870.0214-0.02780.13960.02570.1995-4.693955.738100.6794
41.7046-0.24480.34320.9646-0.19991.3904-0.09380.13720.1367-0.1001-0.0255-0.028-0.07330.17920.10630.1534-0.0284-0.0030.10050.01360.159311.881254.9177108.3468
52.02840.0501-0.14371.7496-0.89071.28340.05470.0608-0.208-0.13740.01560.00360.1511-0.0162-0.03720.14940.0203-0.01690.0795-0.01360.15169.347339.7542115.8356
60.44980.3548-1.11690.00620.43551.8866-0.0649-0.0801-0.10380.0872-0.111-0.06330.31270.19180.14580.28190.05460.01340.27070.05290.18923.849748.146669.618
71.4222-0.44590.45322.0476-0.18181.9785-0.013-0.0473-0.01590.0604-0.0656-0.0098-0.01070.13480.06570.1074-0.0060.02260.19960.02180.1402-1.598263.288460.8629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -13:1)A-13 - 1
2X-RAY DIFFRACTION2chain 'A' and (resseq 2:40)A2 - 40
3X-RAY DIFFRACTION3chain 'A' and (resseq 41:124)A41 - 124
4X-RAY DIFFRACTION4chain 'A' and (resseq 125:204)A125 - 204
5X-RAY DIFFRACTION5chain 'A' and (resseq 205:288)A205 - 288
6X-RAY DIFFRACTION6chain 'B' and (resseq -13:108)B-13 - 108
7X-RAY DIFFRACTION7chain 'B' and (resseq 109:296)B109 - 296

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