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- PDB-3iq0: Crystal structure of a putative Ribokinase II in complex with ATP... -

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Basic information

Entry
Database: PDB / ID: 3iq0
TitleCrystal structure of a putative Ribokinase II in complex with ATP and Mg+2 from E.coli
Componentsputative Ribokinase II
KeywordsTRANSFERASE / KINASE / SAD / RIBOSE / D-RIBOSE METABOLIC PROCESS / RIBOKINASE / PFKB FAMILY / 11206G / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / organic substance metabolic process / phosphorylation / ATP binding
Similarity search - Function
Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Carbohydrate kinase PfkB domain-containing protein / PfkB domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 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 putative Ribokinase (II)in complex with ATP and Mg+2 from E.coli
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative Ribokinase II
B: putative Ribokinase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1937
Polymers73,1062
Non-polymers1,0875
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-41 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.304, 87.256, 112.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative Ribokinase II /


Mass: 36552.852 Da / Num. of mol.: 2 / Fragment: Full length
Source method: isolated from a genetically manipulated source
Details: TOP10 Invitrogen / Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: Escherichia coli O6 / Gene: 1040397, c4014 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+RIL
References: UniProt: Q8FD38, UniProt: A0A0H2VDX9*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris 5.5, 25% PEG 3350, 6mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2008 / 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: 1.79→50 Å / Num. all: 58913 / Num. obs: 58913 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.112 / Net I/σ(I): 4.9
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 5825 / Rsym value: 0.66 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.79→43.63 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2089 -RANDOM
Rwork0.228 ---
all0.246 51839 --
obs0.228 51839 87.7 %-
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---2.7 Å20 Å2
3----1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.79→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 65 261 5028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_degree23.2
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shellResolution: 1.79→1.9 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.399 216 -
Rwork0.377 --
obs-6110 69.8 %

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