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- PDB-4ocp: N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc-1-ph... -

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Basic information

Entry
Database: PDB / ID: 4ocp
TitleN-acetylhexosamine 1-phosphate kinase in complex with GlcNAc-1-phosphate and ADP
ComponentsN-acetylhexosamine 1-phosphate kinase
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


N-acetylhexosamine 1-kinase / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / phosphotransferase activity, alcohol group as acceptor / kinase activity / transferase activity / carbohydrate metabolic process / hydrolase activity / ATP binding
Similarity search - Function
: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-GN1 / N-acetylhexosamine 1-kinase / Phosphotransferase enzyme family protein
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.938 Å
AuthorsLi, T.L. / Wang, K.C. / Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Wu, C.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes.
Authors: Wang, K.C. / Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / Li, T.L.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylhexosamine 1-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4144
Polymers42,6611
Non-polymers7533
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.142, 79.236, 97.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-acetylhexosamine 1-phosphate kinase


Mass: 42660.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: mdsC, BN57_1851 / Production host: Escherichia coli (E. coli)
References: UniProt: T2I3Q3, UniProt: E8MF12*PLUS, N-acetylhexosamine 1-kinase
#2: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2013
RadiationMonochromator: Horizontally focusing single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.938→30 Å / Num. all: 30364 / Num. obs: 30364 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 14.7
Reflection shellResolution: 1.938→2.01 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.74 / Rsym value: 0.489 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OCJ

4ocj


Resolution: 1.938→28.06 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.799 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21547 1620 5.1 %RANDOM
Rwork0.18264 ---
obs0.18426 30364 98.35 %-
all-30364 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.884 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2--0.12 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.938→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 47 284 3107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022882
X-RAY DIFFRACTIONr_bond_other_d0.0010.021888
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.983917
X-RAY DIFFRACTIONr_angle_other_deg0.82334597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34124.275138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19515434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9461517
X-RAY DIFFRACTIONr_chiral_restr0.0620.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.938→1.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 113 -
Rwork0.22 2016 -
obs-30364 98.02 %

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