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- PDB-1zbs: Crystal Structure of the Putative N-acetylglucosamine Kinase (PG1... -

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Basic information

Entry
Database: PDB / ID: 1zbs
TitleCrystal Structure of the Putative N-acetylglucosamine Kinase (PG1100) from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR18
Componentshypothetical protein PG1100
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #160 / : / BadF/BadG/BcrA/BcrD ATPase family / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Abashidze, M. / Kuzin, A. / Vorobiev, S.M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative N-acetylglucosamine Kinase (PG1100) from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR18
Authors: Forouhar, F. / Abashidze, M. / Kuzin, A. / Vorobiev, S.M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PG1100


Theoretical massNumber of molelcules
Total (without water)32,1301
Polymers32,1301
Non-polymers00
Water2,072115
1
A: hypothetical protein PG1100

A: hypothetical protein PG1100


Theoretical massNumber of molelcules
Total (without water)64,2592
Polymers64,2592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)89.506, 89.506, 82.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein hypothetical protein PG1100


Mass: 32129.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: locus_tag="PG1100" / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7MVG4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.1 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 50 mM (Na)3-citrate (pH 4), 16% PEG1K, 100 mM NH4Br, and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 33024 / Num. obs: 32892 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.104 / Net I/σ(I): 19.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3173 / Rsym value: 0.469 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 444760.74 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2979 9.8 %RANDOM
Rwork0.231 ---
all0.234 32892 --
obs0.231 30352 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.9209 Å2 / ksol: 0.30077 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å21.72 Å20 Å2
2---0.14 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 115 2275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 424 9.9 %
Rwork0.264 3862 -
obs-3862 78.9 %

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