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- PDB-4k8k: Crystal structure of probable sugar kinase protein from Rhizobium... -

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Basic information

Entry
Database: PDB / ID: 4k8k
TitleCrystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with 1-(4-methoxyphenyl)-1-cyclopropane and 2-aminoperimidine
Componentssugar kinase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCHCONSORTIUM / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


kinase activity / nucleotide binding
Similarity search - Function
: / 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
1-(4-methoxyphenyl)cyclopropanecarboxylic acid / 1H-perimidin-2-amine / ADENOSINE / : / Probable sugar kinase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with 1-(4-methoxyphenyl)-1-cyclopropane and 2-aminoperimidine
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Structure summary
Revision 1.2Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,16316
Polymers77,7002
Non-polymers2,46314
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-8 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.592, 91.100, 93.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsdimeric

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein sugar kinase


Mass: 38849.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: RHE_CH00135 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q2KDX6

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Non-polymers , 5 types, 760 molecules

#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-1PJ / 1-(4-methoxyphenyl)cyclopropanecarboxylic acid


Mass: 192.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12O3
#4: Chemical
ChemComp-1PK / 1H-perimidin-2-amine


Mass: 183.209 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H9N3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5,25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 111895 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Χ2: 0.979 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.49-1.526.80.59455190.824199.1
1.52-1.546.90.51354800.878199.5
1.54-1.5770.43554860.92199.2
1.57-1.6170.38455580.968199.6
1.61-1.6470.34955231.034199.5
1.64-1.6870.30755450.921199.7
1.68-1.7270.28355440.987199.7
1.72-1.7770.22855320.947199.6
1.77-1.8270.19455630.964199.6
1.82-1.887.10.18155540.991199.7
1.88-1.947.10.14555760.99199.7
1.94-2.027.10.12655891.011199.7
2.02-2.117.20.10855781.009199.9
2.11-2.237.20.09956081.0111100
2.23-2.377.30.08956151.0131100
2.37-2.557.30.08156161.0771100
2.55-2.87.20.07556631.0771100
2.8-3.217.20.06456851.0131100
3.21-4.0470.05657310.937199.7
4.04-506.90.05359300.969199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2324 / WRfactor Rwork: 0.1871 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8097 / SU B: 1.815 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0203 / SU Rfree: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE RESIDUAL FLAT DENSITY BETWEEN ILE-307 AND SER-245 IS DUE TO THE TRACE AMOUNTS OF EXOGENOUS ADP OR ITS ANALOGS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 5501 5 %RANDOM
Rwork0.1806 ---
obs0.1825 109969 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.85 Å2 / Biso mean: 15.313 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0 Å2
2---0.3 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 180 746 5940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195414
X-RAY DIFFRACTIONr_angle_refined_deg1.3062.0127365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64223.633245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61915814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2071547
X-RAY DIFFRACTIONr_chiral_restr0.0860.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214182
X-RAY DIFFRACTIONr_rigid_bond_restr4.26135414
X-RAY DIFFRACTIONr_sphericity_free29.5395231
X-RAY DIFFRACTIONr_sphericity_bonded10.25855812
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 399 -
Rwork0.193 7584 -
all-7983 -
obs--99.19 %
Refinement TLS params.

T23: -0.0004 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4473-0.0377-0.0290.6456-0.08480.39870.0075-0.00640.00020.0039-0.00430.0017-0.00120.0114-0.00320.0056-0.0023-0.00210.02310.000914.1216-7.3389-21.1157
20.3886-0.02380.02210.59560.07240.30930.0045-0.02880.01570.0082-0.00790.0037-0.0085-0.01850.00340.0191-0.00270.00850.04290.008526.231829.0317-21.0586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A - B-10 - 9999
2X-RAY DIFFRACTION2B - A-10 - 9999

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