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- PDB-1spq: Understanding protein lids: Structural analysis of active hinge m... -

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Basic information

Entry
Database: PDB / ID: 1spq
TitleUnderstanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / archae / evolution / flexible loop-6 / TIM / N-hinge
Function / homology
Function and homology information


Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Triosephosphate isomerase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsKursula, I. / Salin, M. / Sun, J. / Norledge, B.V. / Haapalainen, A.M. / Sampson, N.S. / Wierenga, R.K.
CitationJournal: Protein Eng.Des.Sel. / Year: 2004
Title: Understanding protein lids: structural analysis of active hinge mutants in triosephosphate isomerase
Authors: Kursula, I. / Salin, M. / Sun, J. / Norledge, B.V. / Haapalainen, A.M. / Sampson, N.S. / Wierenga, R.K.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)53,4875
Polymers53,1692
Non-polymers3183
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-15 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.706, 57.334, 106.154
Angle α, β, γ (deg.)90.00, 92.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA9 - 188 - 17
21GLYGLYLYSLYSBB9 - 188 - 17
32THRTHRALAALAAA27 - 3126 - 30
42THRTHRALAALABB27 - 3126 - 30
53LEULEUALAALAAA33 - 5732 - 56
63LEULEUALAALABB33 - 5732 - 56
74ILEILEPROPROAA59 - 7058 - 69
84ILEILEPROPROBB59 - 7058 - 69
95GLYGLYILEILEAA72 - 8371 - 82
105GLYGLYILEILEBB72 - 8371 - 82
116ASPASPARGARGAA85 - 9984 - 98
126ASPASPARGARGBB85 - 9984 - 98
137VALVALGLYGLYAA101 - 110100 - 109
147VALVALGLYGLYBB101 - 110100 - 109
158ALAALAGLUGLUAA116 - 133115 - 132
168ALAALAGLUGLUBB116 - 133115 - 132
179ALAALAGLUGLUAA136 - 140135 - 139
189ALAALAGLUGLUBB136 - 140135 - 139
1910ALAALAVALVALAA149 - 154148 - 153
2010ALAALAVALVALBB149 - 154148 - 153
2111GLNGLNGLUGLUAA180 - 186179 - 185
2211GLNGLNGLUGLUBB180 - 186179 - 185
2312LEULEULEULEUAA188 - 192187 - 191
2412LEULEULEULEUBB188 - 192187 - 191
2513SERSERCYSCYSAA203 - 217202 - 216
2613SERSERCYSCYSBB203 - 217202 - 216
2714GLUGLUALAALAAA219 - 246218 - 245
2814GLUGLUALAALABB219 - 246218 - 245
Detailsasymmetric unit contains one biological unit, dimer (chains A and B)

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Components

#1: Protein Triosephosphate isomerase / / TIM


Mass: 26584.365 Da / Num. of mol.: 2 / Mutation: A176K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TPI1 / Plasmid: pBSX1c / Production host: Escherichia coli (E. coli) / Strain (production host): DF502 / References: UniProt: P00940, triose-phosphate isomerase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: PEG 6000, Tris, 2-phosphoglycolate, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2003 / Details: Bent mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.13→40 Å / Num. all: 25864 / Num. obs: 25268 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.062 / Net I/σ(I): 22
Reflection shellResolution: 2.13→2.21 Å / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 7.4 / Num. unique all: 2035 / Rsym value: 0.144 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8TIM

8tim


Resolution: 2.16→38.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.707 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.256 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19779 1270 5 %RANDOM
Rwork0.16023 ---
all0.16215 25268 --
obs0.16215 23998 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.296 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20.92 Å2
2---1.29 Å20 Å2
3---2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.16→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 21 352 4037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213753
X-RAY DIFFRACTIONr_bond_other_d0.0020.023433
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9445055
X-RAY DIFFRACTIONr_angle_other_deg0.85838020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315478
X-RAY DIFFRACTIONr_chiral_restr0.0690.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024169
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02715
X-RAY DIFFRACTIONr_nbd_refined0.1810.2586
X-RAY DIFFRACTIONr_nbd_other0.2210.23350
X-RAY DIFFRACTIONr_nbtor_other0.0790.21877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.27
X-RAY DIFFRACTIONr_mcbond_it0.98332368
X-RAY DIFFRACTIONr_mcangle_it1.58843774
X-RAY DIFFRACTIONr_scbond_it0.96231385
X-RAY DIFFRACTIONr_scangle_it1.50741281
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
1010tight positional0.040.05
1425loose positional0.145
1010tight thermal0.090.5
1425loose thermal0.8110
LS refinement shellResolution: 2.157→2.273 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.203 141
Rwork0.17 2619
obs-2760
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)
11.05110.2856-0.05650.892-0.28250.80160.0195-0.2206-0.0280.07990.00020.0771-0.0315-0.1137-0.01970.2316-0.0003-0.03720.28550.01040.006416.573-12.14439.386
21.0126-0.0808-0.10830.8172-0.11220.70770.01320.10230.1159-0.086-0.02520.1204-0.0975-0.06290.01190.28660.01-0.06710.22860.00790.022123.28212.29514.961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2483 - 247
2X-RAY DIFFRACTION2BB4 - 2483 - 247

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