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- PDB-3vgk: Crystal structure of a ROK family glucokinase from Streptomyces g... -

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Basic information

Entry
Database: PDB / ID: 3vgk
TitleCrystal structure of a ROK family glucokinase from Streptomyces griseus
ComponentsGlucokinase
KeywordsTRANSFERASE / ROK family / glucokinase
Function / homology
Function and homology information


glucokinase / glucokinase activity / glycolytic process / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Glucokinase ROK / ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsMiyazono, K. / Tabei, N. / Morita, S. / Ohnishi, Y. / Horinouchi, S. / Tanokura, M.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus
Authors: Miyazono, K. / Tabei, N. / Morita, S. / Ohnishi, Y. / Horinouchi, S. / Tanokura, M.
History
DepositionAug 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 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_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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Glucokinase
B: Glucokinase
C: Glucokinase
D: Glucokinase
E: Glucokinase
F: Glucokinase
G: Glucokinase
H: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,26518
Polymers267,5498
Non-polymers71510
Water0
1
A: Glucokinase
D: Glucokinase
F: Glucokinase
G: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0368
Polymers133,7754
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucokinase
C: Glucokinase
E: Glucokinase
H: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,22810
Polymers133,7754
Non-polymers4546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.690, 173.700, 124.030
Angle α, β, γ (deg.)90.000, 106.690, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUGLYGLYAA3 - 3133 - 313
2GLYGLYGLYGLYBB2 - 3132 - 313
3LEULEUGLNGLNCC3 - 3123 - 312
4LEULEUGLYGLYDD3 - 3133 - 313
5LEULEUGLNGLNEE3 - 3123 - 312
6LEULEUGLNGLNFF3 - 3123 - 312
7LEULEUGLYGLYGG3 - 3133 - 313

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Components

#1: Protein
Glucokinase /


Mass: 33443.648 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Strain: JCM 4626 / NBRC 13350 / Gene: glkA, SGR_5377 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: B1VZT1, glucokinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCl (pH 7.5), 16% PEG 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→20 Å / Num. obs: 60768 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 76.659 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.25-3.330.9320.8292.1418377468845760.95497.6
3.33-3.430.7130.6612.8317883449344080.7698.1
3.43-3.530.6640.6313.2617678444043260.72397.4
3.53-3.630.6780.5893.1515054426938460.6890.1
3.63-3.750.2510.2726.3614271412637390.31790.6
3.75-3.880.2960.2745.9215785402638590.31595.9
3.88-4.030.2570.2357.0515362386937070.2795.8
4.03-4.20.1570.1529.3115449373636500.17497.7
4.2-4.380.1110.11611.2614851357635080.13298.1
4.38-4.60.0930.09612.7814173344133750.1198.1
4.6-4.840.0850.08613.6413439326432050.09998.2
4.84-5.140.0770.0811412732308330340.09298.4
5.14-5.490.0740.07814.4811990289928570.08998.6
5.49-5.930.0670.07715.1411196270426620.08898.4
5.93-6.50.0580.06816.5110291248324440.07898.4
6.5-7.270.0420.05619.059296225522190.06498.4
7.27-8.390.0330.04822.178186199919720.05598.6
8.39-10.280.0290.04524.456894168816650.05298.6
10.28-14.530.0270.04425.575312132612910.0597.4
14.530.0250.04525.3916657434250.05257.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VGM

3vgm


Resolution: 3.25→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 55.695 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 6121 10.1 %RANDOM
Rwork0.2059 ---
obs0.2119 60748 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 180.96 Å2 / Biso mean: 87.3443 Å2 / Biso min: 53.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-1.54 Å2
2--0.87 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18124 0 18 0 18142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02218460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212375
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.95125029
X-RAY DIFFRACTIONr_angle_other_deg0.919329963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46452477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94223.434792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.556152784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.87915160
X-RAY DIFFRACTIONr_chiral_restr0.0730.22752
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023853
X-RAY DIFFRACTIONr_mcbond_it0.4691.512116
X-RAY DIFFRACTIONr_mcbond_other0.0811.55263
X-RAY DIFFRACTIONr_mcangle_it0.899219057
X-RAY DIFFRACTIONr_scbond_it1.00836344
X-RAY DIFFRACTIONr_scangle_it1.8284.55972
Refine LS restraints NCS

Ens-ID: 1 / Number: 3808 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.540.5
2BMEDIUM POSITIONAL0.50.5
3CMEDIUM POSITIONAL0.640.5
4DMEDIUM POSITIONAL0.580.5
5EMEDIUM POSITIONAL0.530.5
6FMEDIUM POSITIONAL0.520.5
7GMEDIUM POSITIONAL0.70.5
1AMEDIUM THERMAL0.32
2BMEDIUM THERMAL0.322
3CMEDIUM THERMAL0.342
4DMEDIUM THERMAL0.332
5EMEDIUM THERMAL0.322
6FMEDIUM THERMAL0.272
7GMEDIUM THERMAL0.342
LS refinement shellResolution: 3.25→3.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 447 -
Rwork0.322 4006 -
all-4453 -
obs--97.78 %
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)
10.68770.1943-0.3091.7839-0.53952.61830.05120.1135-0.0730.01350.09520.0806-0.1370.0335-0.14640.0111-0.0023-0.00820.04470.01870.082110.829686.43238.8226
21.41120.1538-1.56011.22150.31371.9428-0.05760.0309-0.0110.13380.0911-0.03490.1040.0541-0.03360.1293-0.0169-0.02920.1293-0.08640.076156.223148.145564.2169
32.11880.1692-0.09040.8680.57010.3958-0.0754-0.03790.0263-0.0899-0.03320.1827-0.058-0.00210.10860.0997-0.0516-0.03930.1542-0.10610.150849.7468129.702638.0032
40.57130.42560.18321.30760.85060.58680.04330.25260.0456-0.0959-0.10270.0508-0.0837-0.14890.05930.1140.0892-0.02220.2323-0.03210.077384.9025105.33127.8328
52.4785-0.0341-1.74191.5671-0.79742.51040.0077-0.05220.0725-0.0346-0.02120.18970.0145-0.02360.01350.0476-0.0156-0.02630.0371-0.01550.066888.9032148.350426.6537
60.629-0.37020.04341.76780.7892.48980.1064-0.0651-0.0373-0.0247-0.0133-0.2057-0.190.0056-0.0930.0610.0283-0.04140.1114-0.04890.0723104.528986.641-10.5069
72.70350.66510.15420.7355-0.08950.2367-0.04990.1079-0.0633-0.18490.1395-0.0846-0.0646-0.0121-0.08970.1431-0.06250.03340.0975-0.05170.1485131.6422103.607820.4028
82.88660.3584-0.52182.2839-0.63231.6101-0.1527-0.6477-0.18910.5698-0.0993-0.42140.25070.49460.2520.35190.1364-0.13620.45910.08110.153296.1936131.09653.3836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 313
2X-RAY DIFFRACTION2B2 - 313
3X-RAY DIFFRACTION3C3 - 312
4X-RAY DIFFRACTION4D3 - 313
5X-RAY DIFFRACTION5E3 - 312
6X-RAY DIFFRACTION6F3 - 312
7X-RAY DIFFRACTION7G3 - 313
8X-RAY DIFFRACTION8H3 - 312

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