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- PDB-3bf5: Crystal structure of putative ribokinase (10640157) from Thermopl... -

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Basic information

Entry
Database: PDB / ID: 3bf5
TitleCrystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution
ComponentsRibokinase related protein
KeywordsTRANSFERASE / 10640157 / putative ribokinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


inosine metabolic process / guanosine metabolic process / cytidine kinase / nucleoside kinase activity / inosine kinase / inosine kinase activity / guanosine kinase activity / guanosine binding / cytidine metabolic process / adenosine kinase ...inosine metabolic process / guanosine metabolic process / cytidine kinase / nucleoside kinase activity / inosine kinase / inosine kinase activity / guanosine kinase activity / guanosine binding / cytidine metabolic process / adenosine kinase / adenosine kinase activity / nucleoside phosphate biosynthetic process / adenosine metabolic process / cytidine kinase activity / phosphorylation / GTP binding / ATP binding
Similarity search - Function
: / putative 5-dehydro-2- deoxygluconokinase like fold / putative 5-dehydro-2- deoxygluconokinase / 5-Dehydro-2-deoxygluconokinase-like superfamily / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Single Sheet ...: / putative 5-dehydro-2- deoxygluconokinase like fold / putative 5-dehydro-2- deoxygluconokinase / 5-Dehydro-2-deoxygluconokinase-like superfamily / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Single Sheet / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / PHOSPHATE ION / Nucleoside kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: E112A, K113A, K115A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase related protein
B: Ribokinase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,92210
Polymers71,2942
Non-polymers6288
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 59.180, 177.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: MSE / End label comp-ID: MSE / Refine code: 5 / Auth seq-ID: 1 - 282 / Label seq-ID: 20 - 301

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribokinase related protein


Mass: 35647.117 Da / Num. of mol.: 2 / Mutation: E112A, K113A, K115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM 1728, AMRC-C165, IFO 15155, JCM 9062 / Gene: 10640157, Ta0880 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HJT3
#2: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT WAS ENGINEERED WITH REMARK 999 THE FOLLOWING MUTATIONS: E112A, K113A, K115A.

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979391
30.979531
ReflectionResolution: 1.91→29.185 Å / Num. obs: 46740 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.803 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.78
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.6851.4140809105199.6
1.98-2.060.5271.8138528909199.6
2.06-2.150.3962.4133988550199.5
2.15-2.260.2933.2136808669199.5
2.26-2.410.2194.2147859353199.6
2.41-2.590.1535.9137898585199.3
2.59-2.850.0949143358825198.8
2.85-3.260.04616144788767198.1
3.26-4.10.02427.8145868704197.6
4.1-29.1850.01737.8143608401192.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.91→29.185 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.13 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. 1,2-PROPANEDIOL (PGO) IS MODELED FROM THE CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2364 5.1 %RANDOM
Rwork0.202 ---
obs0.205 46708 99.12 %-
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 mean: 34.325 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2--0.3 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 40 214 4606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224570
X-RAY DIFFRACTIONr_bond_other_d0.0030.023071
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9526183
X-RAY DIFFRACTIONr_angle_other_deg1.27237485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7585588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90923.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18315755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025131
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02970
X-RAY DIFFRACTIONr_nbd_refined0.1670.2750
X-RAY DIFFRACTIONr_nbd_other0.1360.22926
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22168
X-RAY DIFFRACTIONr_nbtor_other0.0720.22292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1560.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.212
X-RAY DIFFRACTIONr_mcbond_it1.63632982
X-RAY DIFFRACTIONr_mcbond_other0.4531165
X-RAY DIFFRACTIONr_mcangle_it2.4254546
X-RAY DIFFRACTIONr_scbond_it4.38781899
X-RAY DIFFRACTIONr_scangle_it5.879111623
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
1630MEDIUM POSITIONAL0.250.5
1899LOOSE POSITIONAL0.385
1630MEDIUM THERMAL0.772
1899LOOSE THERMAL1.9910
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 168 -
Rwork0.306 3240 -
all-3408 -
obs--99.59 %
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)
11.55090.13560.60061.54130.31472.17190.0676-0.1361-0.0190.134-0.01180.0216-0.0673-0.1845-0.0558-0.25730.00440.0037-0.18080.0292-0.052713.46734.85346.025
20.2263-0.3621-0.11680.6340.89649.27170.04790.1053-0.00060.02190.06930.01960.6104-0.388-0.11720.019-0.06470.0031-0.0429-0.0158-0.01628.16931.655-1.379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 28319 - 302
2X-RAY DIFFRACTION2BB1 - 26320 - 282
3X-RAY DIFFRACTION2BB267 - 282286 - 301

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