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- PDB-4gm6: Crystal structure of PfkB family carbohydrate kinase(TARGET EFI-5... -

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Basic information

Entry
Database: PDB / ID: 4gm6
TitleCrystal structure of PfkB family carbohydrate kinase(TARGET EFI-502146 FROM Listeria grayi DSM 20601
ComponentsPfkB family carbohydrate kinase
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / ENZYME FUNCTION INITIATIVE
Function / homology
Function and homology information


: / 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
Biological speciesListeria grayi DSM 20601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of PfkB family carbohydrate kinase FROM Listeria grayi
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: PfkB family carbohydrate kinase
B: PfkB family carbohydrate kinase
C: PfkB family carbohydrate kinase
D: PfkB family carbohydrate kinase
E: PfkB family carbohydrate kinase
F: PfkB family carbohydrate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,76213
Polymers236,2306
Non-polymers5317
Water19,4021077
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-91 kcal/mol
Surface area69080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.832, 109.862, 109.592
Angle α, β, γ (deg.)90.00, 101.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 32025 - 343
21ALAALABB2 - 32025 - 343
12ALAALAAA2 - 32025 - 343
22ALAALACC2 - 32025 - 343
13ALAALAAA2 - 32025 - 343
23ALAALADD2 - 32025 - 343
14ALAALAAA2 - 32025 - 343
24ALAALAEE2 - 32025 - 343
15ALAALAAA2 - 32025 - 343
25ALAALAFF2 - 32025 - 343
16ASPASPBB2 - 32125 - 344
26ALAALACC2 - 32025 - 343
17ASPASPBB2 - 32125 - 344
27ALAALADD2 - 32025 - 343
18ASPASPBB2 - 32125 - 344
28ASPASPEE2 - 32125 - 344
19ALAALABB2 - 32025 - 343
29ALAALAFF2 - 32025 - 343
110LYSLYSCC2 - 32225 - 345
210LYSLYSDD2 - 32225 - 345
111SERSERCC2 - 32325 - 346
211SERSEREE2 - 32325 - 346
112ALAALACC2 - 32025 - 343
212ALAALAFF2 - 32025 - 343
113LYSLYSDD2 - 32225 - 345
213LYSLYSEE2 - 32225 - 345
114ALAALADD2 - 32025 - 343
214ALAALAFF2 - 32025 - 343
115ALAALAEE2 - 32025 - 343
215ALAALAFF2 - 32025 - 343

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
PfkB family carbohydrate kinase


Mass: 39371.715 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria grayi DSM 20601 (bacteria) / Strain: DSM 20601 / Gene: HMPREF0556_10677 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7UWR6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M CALCIUM ACETATE, PH 7.5, 0.1M HEPES-NAOH, 10% PEG8000 , VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 168562 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 4.2 % / Biso Wilson estimate: 32.67 Å2 / Rsym value: 0.069 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0025refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AFB

2afb


Resolution: 2→48.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.629 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5079 3 %RANDOM
Rwork0.175 ---
obs0.176 162516 99.4 %-
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: 51.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.12 Å2
2--1.09 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15140 0 32 1077 16249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915794
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.93721508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15351999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44423.669706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.249152622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9681586
X-RAY DIFFRACTIONr_chiral_restr0.070.22416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4160.17
12B4160.17
21A4130.16
22C4130.16
31A4220.15
32D4220.15
41A4140.16
42E4140.16
51A4160.15
52F4160.15
61B4090.16
62C4090.16
71B4230.16
72D4230.16
81B4190.17
82E4190.17
91B4130.15
92F4130.15
101C4120.14
102D4120.14
111C4110.16
112E4110.16
121C4020.14
122F4020.14
131D4120.15
132E4120.15
141D4140.13
142F4140.13
151E4020.15
152F4020.15
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 373 -
Rwork0.281 11415 -
obs--95.08 %
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)
12.5069-0.5154-0.49481.1069-0.0921.5289-0.0811-0.95190.04960.31950.12840.0868-0.1004-0.1022-0.04740.24080.05070.03110.5151-0.03230.061417.726143.39310.2124
22.15-0.64220.3991.00770.16772.140.12540.92670.0309-0.2957-0.13530.00840.09680.29920.00980.28870.08220.01520.54110.02330.056929.631242.2797-52.5919
32.7112-0.05660.77132.0920.62981.64810.20280.174-1.1257-0.0785-0.00360.03240.4360.0231-0.19930.29670.0157-0.09380.0166-0.07920.587226.370511.8028-22.5331
43.16970.2850.37171.1596-0.32141.65520.02120.00180.41520.0186-0.0644-0.3051-0.1480.49840.04320.1346-0.03970.00570.1694-0.01390.22755.93747.1507-16.2296
51.44890.33660.48761.7328-0.00741.6093-0.1085-0.02540.6428-0.03740.0435-0.0928-0.53480.01890.06510.43290.0166-0.02520.0053-0.02480.494224.518275.6423-21.0964
62.96980.1538-0.67611.1395-0.49341.32160.06540.2488-0.0741-0.09490.0490.3716-0.027-0.5043-0.11450.13850.0432-0.03230.29380.03180.2015-7.321641.6678-24.0422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 321
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION1A501 - 674
4X-RAY DIFFRACTION2B2 - 322
5X-RAY DIFFRACTION2B401 - 403
6X-RAY DIFFRACTION2B501 - 692
7X-RAY DIFFRACTION3C2 - 323
8X-RAY DIFFRACTION3C401 - 571
9X-RAY DIFFRACTION4D2 - 323
10X-RAY DIFFRACTION4D401
11X-RAY DIFFRACTION4D501 - 688
12X-RAY DIFFRACTION5E2 - 323
13X-RAY DIFFRACTION5E401
14X-RAY DIFFRACTION5E501 - 673
15X-RAY DIFFRACTION6F2 - 321
16X-RAY DIFFRACTION6F401 - 579

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