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- PDB-4k6a: Revised Crystal Structure of apo-form of Triosephosphate Isomeras... -

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Basic information

Entry
Database: PDB / ID: 4k6a
TitleRevised Crystal Structure of apo-form of Triosephosphate Isomerase (tpiA) from Escherichia coli at 1.8 Angstrom Resolution.
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM beta/alpha barrel / triose-phosphate isomerase activity
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMinasov, G. / Kuhn, M. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: PLoS ONE / Year: 2014
Title: Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation.
Authors: Kuhn, M.L. / Zemaitaitis, B. / Hu, L.I. / Sahu, A. / Sorensen, D. / Minasov, G. / Lima, B.P. / Scholle, M. / Mrksich, M. / Anderson, W.F. / Gibson, B.W. / Schilling, B. / Wolfe, A.J.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name
Revision 1.2Sep 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5183
Polymers59,4952
Non-polymers231
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-26 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.066, 67.488, 149.769
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 Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 29747.729 Da / Num. of mol.: 2 / Fragment: Triosephosphate Isomerase (tpiA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: ECMDS42_3357, tpiA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: H0QFE6, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D11), 0.2M Calcium chloride, 0.1M Tris-HCl pH 8.0, 20% (w/v) PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03326 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2013 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 44231 / Num. obs: 44231 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2158 / % possible all: 98.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRE

1tre


Resolution: 1.8→29.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.006 / SU ML: 0.071
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 2228 5 %RANDOM
Rwork0.14895 ---
all0.15075 41906 --
obs0.15075 41906 99.85 %-
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: 16.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.16 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 1 546 4333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224175
X-RAY DIFFRACTIONr_bond_other_d0.0010.022752
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9495691
X-RAY DIFFRACTIONr_angle_other_deg0.87836789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7695579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45225.114176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.46915724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2371522
X-RAY DIFFRACTIONr_chiral_restr0.080.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
X-RAY DIFFRACTIONr_mcbond_it0.9731.52737
X-RAY DIFFRACTIONr_mcbond_other0.3291.51124
X-RAY DIFFRACTIONr_mcangle_it1.58424388
X-RAY DIFFRACTIONr_scbond_it2.81531438
X-RAY DIFFRACTIONr_scangle_it4.6644.51303
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 157 -
Rwork0.194 3023 -
obs-2228 98.51 %
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)
10.71110.2294-0.09460.7941-0.01970.59640.0115-0.0562-0.01920.0230.02020.02360.1121-0.009-0.03170.02740.0035-0.00520.02230.00310.00522.5585-22.555717.984
20.8828-0.106-0.30670.89860.29711.49450.0291-0.0753-0.11280.05440.0238-0.00880.25260.0055-0.05290.1073-0.0003-0.00970.01960.02050.029-0.7898-36.175423.7996
30.8950.0856-0.06941.05030.18210.7608-0.0155-0.05130.0332-0.04180.0599-0.006-0.03380.0668-0.04430.01660.01310.00910.0401-0.00530.017414.8202-2.665814.7919
41.0513-0.46960.2251.69190.2031.2193-0.0519-0.10710.1734-0.01230.0959-0.1536-0.22040.1251-0.0440.0545-0.01740.02520.0718-0.03570.068322.58189.414518.528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2A143 - 255
3X-RAY DIFFRACTION3B1 - 142
4X-RAY DIFFRACTION4B143 - 255

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