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- PDB-1xi3: Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu... -

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Basic information

Entry
Database: PDB / ID: 1xi3
TitleThiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001
ComponentsThiamine phosphate pyrophosphorylase
KeywordsTRANSFERASE / structural genomics / Thiamine phosphate pyrophosphorylase / Southeast Collaboratory for Structural Genomics / Pyrococcus furiosus / hyperthermophile / protein structure initiative / PSI / SECSG
Function / homology
Function and homology information


thiamine phosphate synthase / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding
Similarity search - Function
Thiamine phosphate synthase / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Thiamine-phosphate synthase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsZhou, W. / Chen, L. / Tempel, W. / Liu, Z.-J. / Habel, J. / Lee, D. / Lin, D. / Chang, S.-H. / Dillard, B.D. / Eneh, J.C. ...Zhou, W. / Chen, L. / Tempel, W. / Liu, Z.-J. / Habel, J. / Lee, D. / Lin, D. / Chang, S.-H. / Dillard, B.D. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / Kelley, L.-L.C. / Lee, H.-S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Adams, M.W.W. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001
Authors: Zhou, W. / Chen, L. / Tempel, W. / Liu, Z.-J. / Habel, J. / Lee, D. / Lin, D. / Chang, S.-H. / DILLARD, B.D. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / KELLEY, L.-L.C. / Lee, H.-S. / ...Authors: Zhou, W. / Chen, L. / Tempel, W. / Liu, Z.-J. / Habel, J. / Lee, D. / Lin, D. / Chang, S.-H. / DILLARD, B.D. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / KELLEY, L.-L.C. / Lee, H.-S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Adams, M.W.W. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine phosphate pyrophosphorylase
B: Thiamine phosphate pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2217
Polymers47,0662
Non-polymers1555
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-28 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.386, 81.210, 152.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-302-

NI

21A-463-

HOH

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Components

#1: Protein Thiamine phosphate pyrophosphorylase / TMP pyrophosphorylase / TMP-PPase / Thiamine-phosphate synthase


Mass: 23532.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: thiE / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U192, thiamine phosphate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 4.6
Details: 30%v/v PEG 2000 MME, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, modified microbatch, temperature 291KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 50284 / % possible obs: 100 % / Rmerge(I) obs: 0.098 / Χ2: 2.561
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
1.7-1.760.28149611.001100
1.76-1.830.25249501.053100
1.83-1.910.19849981.284100
1.91-2.020.1649941.615100
2.02-2.140.13349892.036100
2.14-2.310.11649742.46100
2.31-2.540.10650482.889100
2.54-2.910.09750303.429100
2.91-3.660.08550734.613100
3.66-300.07452675.054100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1G4T

1g4t


Resolution: 1.7→29.086 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.19 / SU B: 1.787 / SU ML: 0.061 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1540 3.063 %thin shells
Rwork0.188 ---
all0.189 ---
obs0.18878 50281 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.981 Å2
Baniso -1Baniso -2Baniso -3
1-0.012 Å20 Å20 Å2
2--0.004 Å20 Å2
3----0.016 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 9 264 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223079
X-RAY DIFFRACTIONr_bond_other_d0.0020.023034
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9994164
X-RAY DIFFRACTIONr_angle_other_deg0.83136994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79624.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62215561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6051528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_nbd_refined0.2180.2641
X-RAY DIFFRACTIONr_nbd_other0.1860.23073
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21563
X-RAY DIFFRACTIONr_nbtor_other0.0810.21869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.29
X-RAY DIFFRACTIONr_mcbond_it2.60322164
X-RAY DIFFRACTIONr_mcbond_other0.6722832
X-RAY DIFFRACTIONr_mcangle_it3.0933224
X-RAY DIFFRACTIONr_mcangle_other1.87332756
X-RAY DIFFRACTIONr_scbond_it2.96521131
X-RAY DIFFRACTIONr_scbond_other0.88922391
X-RAY DIFFRACTIONr_scangle_it4.3553940
X-RAY DIFFRACTIONr_scangle_other1.82434238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.7370.23770.18734183495
1.737-1.7850.2381540.19234293583
1.785-1.8360.26770.18934023479
1.836-1.8920.2321540.18332233377
1.892-1.9540.211770.17932503327
1.954-2.0220.228770.18630843161
2.022-2.0980.173770.18629953072
2.098-2.1840.1991540.18528312985
2.184-2.280.234770.18327772854
2.28-2.3910.241770.18426452722
2.391-2.5190.205770.18525182595
2.519-2.6710.228770.19223872464
2.671-2.8530.235770.20422622339
2.853-3.0790.235770.21420792156
3.079-3.3700.19420212021
3.37-3.7610.186770.18917541831
3.761-4.3310.17770.16615461623
4.331-5.27500.16713951395
5.275-7.340.27770.20710391116
7.34-29.08600.204686686

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