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- PDB-2hoe: Crystal structure of N-acetylglucosamine kinase (TM1224) from The... -

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Basic information

Entry
Database: PDB / ID: 2hoe
TitleCrystal structure of N-acetylglucosamine kinase (TM1224) from Thermotoga maritima at 2.46 A resolution
ComponentsN-acetylglucosamine kinase
KeywordsTRANSFERASE / TM1224 / N-acetylglucosamine kinase (EC 2.7.1.59) / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


ROK family / ROK family / ArsR-like helix-turn-helix domain / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...ROK family / ROK family / ArsR-like helix-turn-helix domain / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Transcriptional regulator, XylR-related
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of N-acetylglucosamine kinase (EC 2.7.1.59) (TM1224) from Thermotoga maritima at 2.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.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.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0013
Polymers42,8701
Non-polymers1312
Water27015
1
A: N-acetylglucosamine kinase
hetero molecules

A: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0026
Polymers85,7392
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+2/31
Buried area4170 Å2
ΔGint-18 kcal/mol
Surface area30990 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.599, 62.599, 173.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein N-acetylglucosamine kinase


Mass: 42869.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1224 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0V1, N-acetylglucosamine kinase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Description: REFLECTIONS WITHIN THE 3.72-3.63 ANGSTROM RANGE WERE EXCLUDED FROM DATA PROCESSING BECAUSE OF AN ICE RING.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 0.2M KThioCyanate, 20.0% PEG-3350, No Buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.891940, 0.979083, 0.979251
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2004 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.891941
20.9790831
30.9792511
ReflectionResolution: 2.46→46.029 Å / Num. obs: 14118 / % possible obs: 96.7 % / Redundancy: 5.42 % / Biso Wilson estimate: 47.99 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.46-2.550.911.7969861464134591.9
2.55-2.650.8042.09779714151415100
2.65-2.770.6732.57791114241424100
2.77-2.920.513.36813114681468100
2.92-3.10.3664.69796014341434100
3.1-3.340.246.85798514461446100
3.34-3.670.1639.5570411436129790.3
3.67-4.20.08815.669421480128486.8
4.2-5.270.05821.677821457145399.7
5.27-460.04823.380031576155298.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.46→33.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / SU B: 24.752 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.547 / ESU R Free: 0.307
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ELECTRON DENISTY FOR RESIDUES 31-38, 263-265, 273-275 WAS DIFFICULT TO INTERPRET AND MAY BE POORLY MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 710 5 %RANDOM
Rwork0.216 ---
obs0.219 14086 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.46→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 7 15 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222705
X-RAY DIFFRACTIONr_bond_other_d0.0010.022508
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9693663
X-RAY DIFFRACTIONr_angle_other_deg0.62535786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1085351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58924.528106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41715444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2431511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023026
X-RAY DIFFRACTIONr_gen_planes_other00.02530
X-RAY DIFFRACTIONr_nbd_refined0.2290.2590
X-RAY DIFFRACTIONr_nbd_other0.1910.22433
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21392
X-RAY DIFFRACTIONr_nbtor_other0.0860.21396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.256
X-RAY DIFFRACTIONr_metal_ion_refined0.140.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.25
X-RAY DIFFRACTIONr_mcbond_it1.18331745
X-RAY DIFFRACTIONr_mcbond_other0.2113726
X-RAY DIFFRACTIONr_mcangle_it2.25652793
X-RAY DIFFRACTIONr_scbond_it4.1278972
X-RAY DIFFRACTIONr_scangle_it6.24911870
LS refinement shellResolution: 2.464→2.528 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 47 -
Rwork0.321 978 -
obs-1025 97.16 %
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)
17.63521.2902-1.28292.9598-0.64582.22660.2444-0.48140.27560.1208-0.01190.3782-0.1001-0.2862-0.23250.12210.05190.02210.1458-0.01330.1694-46.46743.49739.473
21.36360.3262-0.71774.6126-2.8723.13330.1761-0.19050.14270.0987-0.1933-0.174-0.12040.24480.01720.03260.0445-0.00250.1112-0.0730.0477-35.53837.46648.275
31.7968-0.4187-0.47023.2791-1.47053.1958-0.12160.0121-0.1598-0.7702-0.3091-0.71320.96770.66920.43070.43390.29180.15650.2481-0.00550.3032-27.59516.14443.654
411.2443-7.3831-4.643412.32014.36924.7403-0.2474-1.15490.41590.18650.36230.5626-0.11660.1043-0.1148-0.00920.07690.01690.2385-0.02670.1525-45.61943.94245.27
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1110 - 13122 - 143
22132 - 236144 - 248
33237 - 348249 - 360
44349 - 368361 - 380

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