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- PDB-1pw5: putative nagD protein -

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Basic information

Entry
Database: PDB / ID: 1pw5
Titleputative nagD protein
ComponentsnagD protein, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / nagD protein / T. maritima / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphatase activity / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / NagD protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsCuff, M.E. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: putative nagD protein
Authors: Cuff, M.E. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJun 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
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 / 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.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nagD protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9734
Polymers28,5601
Non-polymers4133
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.788, 97.788, 159.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein nagD protein, putative


Mass: 28559.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1742 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X264
#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: amonium sulfate, sodium cacodylate, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929,0.97918,0.96396
DetectorType: SBC-2 / Detector: CCD / Date: Jul 26, 2002
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979181
30.963961
ReflectionResolution: 2.8→28.93 Å / Num. all: 18344 / Num. obs: 18344 / Observed criterion σ(F): 0 / Biso Wilson estimate: 70.6 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 24 / Limit k min: 0 / Limit l max: 56 / Limit l min: 0 / Observed criterion F max: 127621.03 / Observed criterion F min: 0.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
RefinementResolution: 2.8→28.93 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
Details: The authors state there is extra electron density near/in the main chain between residues A239 and A242. It could be an extra amino acid (cloning artifact), or some sort of ligand or ligands. ...Details: The authors state there is extra electron density near/in the main chain between residues A239 and A242. It could be an extra amino acid (cloning artifact), or some sort of ligand or ligands. The authors are confident of the chain trace.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 844 5 %RANDOM
Rwork0.244 ---
all-19675 --
obs-16773 85.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 54.6016 Å2 / ksol: 0.297685 e/Å3
Displacement parametersBiso max: 150.17 Å2 / Biso mean: 75.24 Å2 / Biso min: 29.03 Å2
Baniso -1Baniso -2Baniso -3
1-15.85 Å20 Å20 Å2
2--15.85 Å20 Å2
3----31.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.73 Å
Luzzati d res high-2.8
Refinement stepCycle: LAST / Resolution: 2.8→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 25 88 2095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg24
X-RAY DIFFRACTIONx_torsion_impr_deg0.93
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.930.472614.80.44612190.062397128053.4
2.93-3.080.435955.40.39316590.0452413175472.7
3.08-3.270.337954.60.3219840.0352418207986
3.27-3.530.3061034.70.29120830.032426218690.1
3.53-3.880.2791064.60.24921770.0272435228393.8
3.88-4.440.2571295.50.20722220.0232472235195.1
4.44-5.590.231285.40.18722500.022478237896
5.59-28.930.2661275.20.23323350.0242644246293.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1carbohydrate.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4ion.top

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