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- PDB-3pl2: Crystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl... -

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Basic information

Entry
Database: PDB / ID: 3pl2
TitleCrystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl0158) from Corynebacterium glutamicum ATCC 13032 KITASATO at 1.89 A resolution
ComponentsSugar kinase, ribokinase family
KeywordsTRANSFERASE / PFKB PFAM MOTIF / INOSITOL PHOSPHATE METABOLISM / RIBOKINASE-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


fructokinase / fructokinase activity
Similarity search - Function
5-Dehydro-2-deoxygluconokinase / putative 5-dehydro-2- deoxygluconokinase like fold / putative 5-dehydro-2- deoxygluconokinase / 5-Dehydro-2-deoxygluconokinase-like superfamily / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Single Sheet ...5-Dehydro-2-deoxygluconokinase / putative 5-dehydro-2- deoxygluconokinase like fold / putative 5-dehydro-2- deoxygluconokinase / 5-Dehydro-2-deoxygluconokinase-like superfamily / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Single Sheet / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Sugar kinases, ribokinase family
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl0158) from Corynebacterium glutamicum ATCC 13032 KITASATO at 1.89 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar kinase, ribokinase family
B: Sugar kinase, ribokinase family
C: Sugar kinase, ribokinase family
D: Sugar kinase, ribokinase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4825
Polymers140,2904
Non-polymers1921
Water10,395577
1
A: Sugar kinase, ribokinase family
B: Sugar kinase, ribokinase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3373
Polymers70,1452
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area23070 Å2
MethodPISA
2
C: Sugar kinase, ribokinase family
D: Sugar kinase, ribokinase family


Theoretical massNumber of molelcules
Total (without water)70,1452
Polymers70,1452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.908, 79.494, 81.703
Angle α, β, γ (deg.)101.860, 95.720, 92.110
Int Tables number1
Space group name H-MP1
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Sugar kinase, ribokinase family / Sugar kinases / ribokinase family / 5-keto-2-deoxygluconokinase


Mass: 35072.453 Da / Num. of mol.: 4 / Fragment: sequence database residues 22-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: iolC, Cgl0158, cg0197 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NTZ3, fructokinase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.200M NH4OAc, 30.00% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94645 Å / Relative weight: 1
ReflectionResolution: 1.89→37.804 Å / Num. all: 87262 / Num. obs: 87262 / % possible obs: 97.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 25.396 Å2 / Rsym value: 0.065 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.89-1.9420.4381.21261363860.43895.8
1.94-1.9920.31621246063140.31696.1
1.99-2.0520.2343.11183259850.23496.1
2.05-2.1120.21431170258910.21496.4
2.11-2.1820.1584.61140057540.15896.5
2.18-2.2620.1375.11094755240.13796.6
2.26-2.3420.1215.81058553370.12196.8
2.34-2.4420.1026.91032751960.10297
2.44-2.5520.0778.5990049860.07797.1
2.55-2.6720.077.8938647220.0797.4
2.67-2.8220.05512.2901645350.05597.5
2.82-2.9920.04613.7853142870.04697.8
2.99-3.1920.04115.8797140110.04197.7
3.19-3.4520.03715.5754637890.03797.9
3.45-3.783.50.07671209234760.07698.4
3.78-4.233.80.0678.11182831460.06798.5
4.23-4.883.80.068.21049727600.0698.7
4.88-5.983.80.0579.8896123590.05798.9
5.98-8.453.90.0548.2707018140.05499
8.45-37.8043.90.068.238689900.0697.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCV

2qcv


Resolution: 1.89→37.804 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.55 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. CITRIC ACID (CIT) FROM THE CRYSTALLIZATION SOLUTION IS MODELED. 7. RAMACHANDRAN OUTLIER RESIDUE ASP 172 IS WELL SUPPORTED BY DENSITY IN ALL CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 4384 5 %RANDOM
Rwork0.1805 ---
obs0.1828 87222 96.98 %-
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 max: 87.38 Å2 / Biso mean: 37.5491 Å2 / Biso min: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.42 Å20.14 Å2
2---0.49 Å20.53 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.89→37.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 0 13 577 10070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229993
X-RAY DIFFRACTIONr_bond_other_d0.0030.026682
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.96313666
X-RAY DIFFRACTIONr_angle_other_deg1.327316313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69151322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53524.072474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.591151589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7371574
X-RAY DIFFRACTIONr_chiral_restr0.0910.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111452
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022058
X-RAY DIFFRACTIONr_mcbond_it0.6811.56287
X-RAY DIFFRACTIONr_mcbond_other0.1821.52554
X-RAY DIFFRACTIONr_mcangle_it1.211210143
X-RAY DIFFRACTIONr_scbond_it1.93833706
X-RAY DIFFRACTIONr_scangle_it3.1214.53479
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 325 -
Rwork0.245 5912 -
all-6237 -
obs--93.86 %
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)
11.23210.0715-0.44780.9813-0.91351.57060.05210.30760.0242-0.10170.01550.18230.1631-0.1038-0.06760.11370.05190.01140.16470.0160.058825.56560.51736.316
20.9740.10630.31691.15320.47441.8441-0.0173-0.0814-0.0771-0.02520.0008-0.08870.1010.17150.01650.0370.05470.02780.09140.04860.040334.98161.60377.848
30.85890.3912-0.26472.6399-1.1791.34570.1498-0.0532-0.05360.26-0.00050.3405-0.1629-0.0381-0.14930.05730.02330.02590.06270.02620.123324.37323.16672.705
41.1522-0.6242-0.44781.12721.4452.86560.05260.12840.1566-0.12650.0417-0.0927-0.26490.2048-0.09430.04320.01030.01320.12490.01920.029543.5321.77333.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 315
2X-RAY DIFFRACTION2B6 - 315
3X-RAY DIFFRACTION3C6 - 315
4X-RAY DIFFRACTION4D6 - 314

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