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- PDB-2vhl: The Three-dimensional structure of the N-Acetylglucosamine-6- pho... -

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Basic information

Entry
Database: PDB / ID: 2vhl
TitleThe Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from Bacillus subtilis
ComponentsN-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
KeywordsHYDROLASE / N- ACETYLEGLUCOSAMINE-6-PHOSPHATE / CARBOHYDRATE METABOLISM / DEACETYLASE / BACILLUS SUBTILIS
Function / homology
Function and homology information


N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / iron ion binding / protein homodimerization activity
Similarity search - Function
BsNagA composite domain / N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...BsNagA composite domain / N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Chem-GLP / TRIETHYLENE GLYCOL / N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVincent, F. / Yates, D. / Garman, E. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Three-Dimensional Structure of the N-Acetylglucosamine-6-Phosphate Deacetylase from Bacillus Subtilis
Authors: Vincent, F. / Yates, D. / Garman, E. / Davies, G.J.
History
DepositionNov 22, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionDec 4, 2007ID: 1UN7
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 24, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_assembly.method_details ..._chem_comp.pdbx_synonyms / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
B: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,39110
Polymers85,3492
Non-polymers1,0428
Water11,169620
1
A: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
hetero molecules

A: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,39110
Polymers85,3492
Non-polymers1,0428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4660 Å2
ΔGint-61 kcal/mol
Surface area27900 Å2
MethodPISA
2
B: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
hetero molecules

B: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,39110
Polymers85,3492
Non-polymers1,0428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4650 Å2
ΔGint-64 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.680, 107.740, 188.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE / GLCNAC 6-P DEACETYLASE


Mass: 42674.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AUTHORS ACKNOWLEDGE DR. DAAN VAN AALTEN FOR FOR INDICATING ERROR IN THEIR PDB ENTRY 1UN7
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): IG20
References: UniProt: O34450, N-acetylglucosamine-6-phosphate deacetylase
#2: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.83 Å3/Da / Density % sol: 56.19 % / Description: NONE
Crystal growDetails: 8% PEG 20K (W/V), 8% PEG 550 MME (V/V), 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 71574 / % possible obs: 97.4 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.36 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O12

1o12


Resolution: 2.05→21.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.812 / SU ML: 0.131 / σ(F): 2 / ESU R: 0.186 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3328 5.16 %RANDOM
Rwork0.205 ---
obs0.208 65440 97.7 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.027 Å20 Å20 Å2
2---0.009 Å20 Å2
3----0.018 Å2
Refinement stepCycle: LAST / Resolution: 2.05→21.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5931 0 56 620 6607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226088
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9698231
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50824.818247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.666151057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2761528
X-RAY DIFFRACTIONr_chiral_restr0.1240.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024472
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.23003
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24112
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2595
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9681.54015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54626222
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.47332340
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7734.52009
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: 8.48→21.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 63
Rwork0.236 885

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