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- PDB-1aw2: TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS -

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Basic information

Entry
Database: PDB / ID: 1aw2
TitleTRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / PSYCHROPHILIC / VIBRIO MARINUS
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
Triosephosphate isomerase
Similarity search - Component
Biological speciesMoritella marina (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMaes, D. / Zeelen, J.P. / Wierenga, R.K.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.
Authors: Alvarez, M. / Zeelen, J.P. / Mainfroid, V. / Rentier-Delrue, F. / Martial, J.A. / Wyns, L. / Wierenga, R.K. / Maes, D.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
J: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,51412
Polymers214,1308
Non-polymers3844
Water3,099172
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area18960 Å2
MethodPISA
2
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area18970 Å2
MethodPISA
3
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-31 kcal/mol
Surface area18960 Å2
MethodPISA
4
J: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.660, 137.820, 89.540
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.007, 0.006, 1), (0.004, 1, -0.006), (-1, 0.004, 0.007)-0.85298, 34.55416, 88.58136
2given(1, -0.003, 0.01), (-0.004, -1, 0.006), (0.01, -0.006, -1)-0.49083, 102.28472, 88.97144
3given(-0.016, 1), (-1), (1, 0.016)0.02818, 67.90625, 0.01734

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE


Mass: 26766.199 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: A SULFATE MOLECULE IS OBSERVED IN THE ACTIVE SITE OF SUBUNIT A
Source: (gene. exp.) Moritella marina (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P50921, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growpH: 7
Details: 100MM TRIETHANOLAMINE/HCL 100MM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 1.26M SODIUM CITRATE PH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMtriethanolamine-HCl1reservoir
325 mM1reservoirNaCl
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir
61 mM1reservoirNaN3
720 mM2PG1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: DOUBLE FOCUSSING MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 60048 / % possible obs: 95.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 11
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 6.7 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 166818
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LIGANDED STRUCTURE (PDB ENTRY 1AFI)

1afi


Resolution: 2.65→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 -5 %RANDOM
Rwork0.2 ---
obs0.2 57974 95.7 %-
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 5 43 3781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 -5 %
Rwork0.29 6576 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64
LS refinement shell
*PLUS
Rfactor obs: 0.29

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