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- PDB-3k5w: Crystal structure of a Carbohydrate kinase (YjeF family)from Heli... -

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Basic information

Entry
Database: PDB / ID: 3k5w
TitleCrystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori
ComponentsCarbohydrate kinase
KeywordsTRANSFERASE / KINASE / SAD / PFKB FAMILY / Carbohydrate kinase / 11206b / Helicobacter pylori / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


NAD(P)H-hydrate epimerase / metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NAD(P)HX epimerase activity / : / nicotinamide nucleotide metabolic process / ATP binding / metal ion binding
Similarity search - Function
Bifunctional NAD(P)H-hydrate repair enzyme Nnr / YjeF N-terminal domain / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / Carbohydrate kinase / YjeF C-terminal domain profile. / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily ...Bifunctional NAD(P)H-hydrate repair enzyme Nnr / YjeF N-terminal domain / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / Carbohydrate kinase / YjeF C-terminal domain profile. / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Bifunctional NAD(P)H-hydrate repair enzyme Nnr
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5092
Polymers52,4141
Non-polymers951
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbohydrate kinase
hetero molecules

A: Carbohydrate kinase
hetero molecules

A: Carbohydrate kinase
hetero molecules

A: Carbohydrate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,0388
Polymers209,6584
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11520 Å2
ΔGint-59 kcal/mol
Surface area72430 Å2
MethodPISA
3
A: Carbohydrate kinase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)420,07616
Polymers419,3168
Non-polymers7608
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area31270 Å2
ΔGint-148 kcal/mol
Surface area136630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.955, 119.955, 162.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Carbohydrate kinase


Mass: 52414.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TOP10 (Invitrogen) / Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: 900323 / Plasmid: pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) CODON + RIL / References: UniProt: P56176
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE REFERENCE TO UNP P56176 IS CORRECT AND THE DIFFERENCES ARE DUE TO NATURAL ...AUTHORS STATE THAT THE REFERENCE TO UNP P56176 IS CORRECT AND THE DIFFERENCES ARE DUE TO NATURAL VARIANT STRAIN. THEY ARE NATURAL VARIANT AND NOT ENGINEERED.

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M KH2PO4, 0.2M Ammonium Citrate pH 7.0 8% Acetonitrile 15% PEG 3,350., VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 25967 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.1 % / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.089 / Net I/σ(I): 10.8
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 27.9 % / Mean I/σ(I) obs: 7.8 / Rsym value: 0.65 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXS& SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→48.23 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Authors state that the number of reflections are correct. Authors have used anomalous pairs as independent reflections in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1302 -RANDOM
Rwork0.233 ---
all0.233 ---
obs0.233 25164 96.5 %-
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 5 79 3619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d0.009
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.367 206 -
Rwork0.323 --
obs--87 %

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