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- PDB-2bkv: Structure and kinetics of a monomeric glucosamine-6-phosphate dea... -

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Basic information

Entry
Database: PDB / ID: 2bkv
TitleStructure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsHYDROLASE / SUBSTRATE INHIBITION / FRUCTOSE-6-PHOSPHATE
Function / homology
Function and homology information


glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / Glucosamine-6-phosphate deaminase 1
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVincent, F. / Davies, G.J. / Brannigan, J.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Kinetics of a Monomeric Glucosamine 6-Phosphate Deaminase: Missing Link of the Nagb Superfamily
Authors: Vincent, F. / Davies, G.J. / Brannigan, J.A.
History
DepositionFeb 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4May 1, 2024Group: Advisory / Category: database_PDB_caveat

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3634
Polymers54,0512
Non-polymers3122
Water6,792377
1
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1812
Polymers27,0251
Non-polymers1561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1812
Polymers27,0251
Non-polymers1561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.009, 48.023, 71.761
Angle α, β, γ (deg.)90.00, 91.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLUCOSAMINE-6-PHOSPHATE DEAMINASE / GLUCOSAMINE-6-PHOSPHATE ISOMERASE 1 / GLCN6P DEAMINASE 1


Mass: 27025.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: IG20 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O35000, glucosamine-6-phosphate deaminase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 1.9 Å3/Da / Density % sol: 36 %

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9168
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 67231 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.6 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB EBTRY 1DEA

1dea


Resolution: 1.5→72.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.646 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3401 5.11 %RANDOM
Rwork0.165 ---
obs0.167 67204 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.632 Å20 Å2-0.434 Å2
2---0.119 Å20 Å2
3---0.736 Å2
Refinement stepCycle: LAST / Resolution: 1.5→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 16 377 4182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9655338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85924.07199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66715729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1111535
X-RAY DIFFRACTIONr_chiral_restr0.190.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2862
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22017
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0581.53097
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41823917
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.19331717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4914.51421
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: 6.7→72.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 49
Rwork0.316 748
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)
10.85550.16270.15190.20050.03480.1302-0.01910.0613-0.02860.02050.01910.0222-0.03260.02880-0.0105-0.00030.01-0.0099-0.0037-0.032228.30522.169-16.101
20.3129-0.031-0.00660.2317-0.03770.19210.0062-0.03050.0058-0.00970.00350.00660.00470.0057-0.0098-0.0038-0.00090.0076-0.0052-0.0019-0.029559.813-0.841-19.622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 241
2X-RAY DIFFRACTION2B1 - 241

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