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- PDB-2nlx: Crystal structure of the apo E. coli xylulose kinase -

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Basic information

Entry
Database: PDB / ID: 2nlx
TitleCrystal structure of the apo E. coli xylulose kinase
ComponentsXylulose kinase
KeywordsTRANSFERASE / xylulokinase / FGGY kinase / ATPase / xylulose / kinase
Function / homology
Function and homology information


1-deoxy-D-xylulose kinase activity / D-xylulokinase activity / xylulokinase / xylulose catabolic process / D-xylose catabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / protein homodimerization activity / ATP binding
Similarity search - Function
Xylulokinase / FGGY family of carbohydrate kinases signature 1. / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain ...Xylulokinase / FGGY family of carbohydrate kinases signature 1. / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
Authorsdi Luccio, E. / Voegtli, J. / Wilson, D.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli.
Authors: Di Luccio, E. / Petschacher, B. / Voegtli, J. / Chou, H.T. / Stahlberg, H. / Nidetzky, B. / Wilson, D.K.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylulose kinase
B: Xylulose kinase


Theoretical massNumber of molelcules
Total (without water)105,3382
Polymers105,3382
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area36150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.780, 112.020, 138.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLNGLNAA1 - 761 - 76
21METMETGLNGLNBB1 - 761 - 76
32METMETLEULEUAA77 - 15077 - 150
42METMETLEULEUBB77 - 15077 - 150
53LEULEUMETMETAA151 - 160151 - 160
63LEULEUMETMETBB151 - 160151 - 160
74THRTHRTHRTHRAA161 - 224161 - 224
84THRTHRTHRTHRBB161 - 224161 - 224
95VALVALGLYGLYAA225 - 242225 - 242
105VALVALGLYGLYBB225 - 242225 - 242
116METMETTRPTRPAA243 - 300243 - 300
126METMETTRPTRPBB243 - 300243 - 300
137ALAALAASNASNAA301 - 359301 - 359
147ALAALAASNASNBB301 - 359301 - 359
158GLUGLUTHRTHRAA360 - 418360 - 418
168GLUGLUTHRTHRBB360 - 418360 - 418
179GLYGLYMETMETAA419 - 483419 - 483
189GLYGLYLEULEUBB419 - 482419 - 482

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Components

#1: Protein Xylulose kinase / Xylulokinase


Mass: 52669.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xylB / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21* / References: UniProt: P09099, xylulokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Drops containing equal volume of 26 mg/ml protein solution mixed with the precipitant solution containing 1.5 M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, VAPOR DIFFUSION, ...Details: Drops containing equal volume of 26 mg/ml protein solution mixed with the precipitant solution containing 1.5 M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2004 / Details: Vertical focusing mirror
RadiationMonochromator: single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.7→24.88 Å / Num. all: 29677 / Num. obs: 29677 / % possible obs: 10.09 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection scaleGroup code: 1
Reflection shellResolution: 2.7→24.88 Å / % possible all: 10

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→24.88 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / SU B: 12.307 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25417 1182 4.1 %RANDOM
Rwork0.20482 ---
obs0.20681 27537 96.77 %-
all-28719 --
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: 33.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---1.1 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 0 158 7394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227397
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9610056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.82224.214318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5391548
X-RAY DIFFRACTIONr_chiral_restr0.1460.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3390.24020
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.25122
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.2343
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2270.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5720.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4351.54765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.69127497
X-RAY DIFFRACTIONr_scbond_it11.70632950
X-RAY DIFFRACTIONr_scangle_it14.4194.52559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1888medium positional0.980.5
1717loose positional1.195
1888medium thermal7.472
1717loose thermal10.6110
LS refinement shellResolution: 2.7→2.844 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.303 180 -
Rwork0.249 3703 -
obs--92.01 %

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