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- PDB-3in1: Crystal structure of a putative Ribokinase in complex with ADP fr... -

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Basic information

Entry
Database: PDB / ID: 3in1
TitleCrystal structure of a putative Ribokinase in complex with ADP from E.coli
ComponentsUncharacterized sugar kinase ydjH
KeywordsTRANSFERASE / RIBOKINASE / PFKB FAMILY / SUGAR KINASE YDJH / ADP NYSGXRC / 11206A / PSI2 / Kinase / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


carbohydrate kinase activity / 2-dehydro-3-deoxygluconokinase activity / D-galacturonate catabolic process / D-glucuronate catabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / DNA damage response / protein homodimerization activity / cytosol
Similarity search - Function
Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / 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'-DIPHOSPHATE / Uncharacterized sugar kinase YdjH
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.15 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 in complex with ADP from E.coli
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 11, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized sugar kinase ydjH
B: Uncharacterized sugar kinase ydjH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3006
Polymers71,3992
Non-polymers9004
Water3,513195
1
A: Uncharacterized sugar kinase ydjH
hetero molecules

B: Uncharacterized sugar kinase ydjH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3006
Polymers71,3992
Non-polymers9004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
Buried area4980 Å2
ΔGint-57 kcal/mol
Surface area24840 Å2
MethodPISA
2
B: Uncharacterized sugar kinase ydjH
hetero molecules

A: Uncharacterized sugar kinase ydjH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3006
Polymers71,3992
Non-polymers9004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
Unit cell
Length a, b, c (Å)75.577, 88.301, 116.608
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 Uncharacterized sugar kinase ydjH


Mass: 35699.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TOP10 Invitrogen / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: strain K12 / Gene: b1772, JW5289, ydjH, ydjH/B1772/JW5289 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: P77493, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 292 K / pH: 5.6
Details: 0.2M AMMONIUM ACETATE, 30% PEG 4K, SODIUM CITRATE 5.6PH, 10% ISOPROPANOL, 10MM ADP sodium salt, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 43219 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 7.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.615 / % possible all: 96.4

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLREP
Starting model: PDB ENTRY 3H49

3h49


Resolution: 2.15→40.29 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1642 -RANDOM
Rwork0.226 ---
obs0.226 40897 94.7 %-
all-40897 --
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.15 Å20 Å20 Å2
2---1.366 Å20 Å2
3----3.784 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.15→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 56 195 4987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
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_it1.4751.5
X-RAY DIFFRACTIONc_mcangle_it2.3492
X-RAY DIFFRACTIONc_scbond_it2.6762
X-RAY DIFFRACTIONc_scangle_it3.9312.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.32 272 -
Rwork0.271 --
obs--86.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ADP.par.txt

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