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- PDB-3jr1: Crystal structure of Putative fructosamine-3-kinase (YP_719053.1)... -

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Basic information

Entry
Database: PDB / ID: 3jr1
TitleCrystal structure of Putative fructosamine-3-kinase (YP_719053.1) from HAEMOPHILUS SOMNUS 129PT at 2.32 A resolution
ComponentsPutative fructosamine-3-kinase
KeywordsTRANSFERASE / YP_719053.1 / Putative fructosamine-3-kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Fructosamine kinase
Function / homology
Function and homology information


Fructosamine/Ketosamine-3-kinase / Fructosamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Fructosamine kinase
Similarity search - Component
Biological speciesHaemophilus somnus 129PT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative fructosamine-3-kinase (YP_719053.1) from HAEMOPHILUS SOMNUS 129PT at 2.32 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Putative fructosamine-3-kinase
B: Putative fructosamine-3-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2417
Polymers74,0552
Non-polymers1865
Water2,918162
1
A: Putative fructosamine-3-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1524
Polymers37,0271
Non-polymers1243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative fructosamine-3-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0903
Polymers37,0271
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.308, 85.627, 99.009
Angle α, β, γ (deg.)90.000, 132.920, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTYRTYR4AA-5 - 26914 - 288
21ASNASNTYRTYR4BB-5 - 26914 - 288
12TYRTYRSERSER6AA270 - 275289 - 294
22TYRTYRSERSER6BB270 - 275289 - 294
13TYRTYRHISHIS4AA276 - 289295 - 308
23TYRTYRHISHIS4BB276 - 289295 - 308

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Components

#1: Protein Putative fructosamine-3-kinase


Mass: 37027.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus somnus 129PT (bacteria) / Strain: 129Pt / Gene: HS_0843, YP_719053.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0I3M3
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY THE ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 5.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0, Additive: 0.001 M Adenosine 5'-[gamma-thio]triphosphate, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.979221
ReflectionResolution: 2.32→27.671 Å / Num. obs: 36282 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.514 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 5.93
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.32-2.40.5461.613119667396.3
2.4-2.50.4761.914135720796.4
2.5-2.610.4072.213209671496.1
2.61-2.750.3132.813901707696.8
2.75-2.920.2553.313506687696.8
2.92-3.150.1734.813957709696.9
3.15-3.460.1176.813454684197
3.46-3.960.0729.913858704897.2
3.96-4.980.05512.513847703897.8
4.980.05213.413788702495.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.32→27.671 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 15.419 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ETHYLENE GLYCRL (EDO) USED AS CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 4. UNKNOWN LIGANDS (UNL) WERE MODELED INTO THE PUTATIVE ACTIVE SITES ON BOTH SUBUNITS IN THE ASYMMETRIC UNIT. 5. TLS PARAMETERS WERE ASSIGNED WITH THE AID OF THE TLS MOTION SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1813 5 %RANDOM
Rwork0.199 ---
obs0.202 36280 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.17 Å2 / Biso mean: 26.01 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-1.64 Å2
2---0.23 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.32→27.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 0 32 162 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225053
X-RAY DIFFRACTIONr_bond_other_d0.0020.023378
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9346871
X-RAY DIFFRACTIONr_angle_other_deg1.0138225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2545607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36124.769260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24415836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2281516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_mcbond_it0.97922970
X-RAY DIFFRACTIONr_mcbond_other0.17721199
X-RAY DIFFRACTIONr_mcangle_it1.9644799
X-RAY DIFFRACTIONr_scbond_it3.24162083
X-RAY DIFFRACTIONr_scangle_it4.58182063
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3903MEDIUM POSITIONAL0.230.5
63LOOSE POSITIONAL1.165
3903MEDIUM THERMAL0.512
63LOOSE THERMAL0.6110
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 124 -
Rwork0.276 2566 -
all-2690 -
obs--99.26 %
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5562-0.07720.20420.5895-0.14510.47030.01480.0708-0.0216-0.0664-0.0161-0.0220.05790.04710.00140.1478-0.00290.01280.1425-0.01250.13347.007439.14938.3679
20.490.16150.24830.53840.06820.5336-0.0003-0.04260.05860.018-0.01470.063-0.0282-0.06840.01510.12110.01230.01260.12880.00240.135977.170120.233849.1759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 290
2X-RAY DIFFRACTION2B-5 - 289

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