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- PDB-1aw1: TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS COMPLEXED WITH 2-PHOS... -

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Basic information

Entry
Database: PDB / ID: 1aw1
TitleTRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS COMPLEXED WITH 2-PHOSPHOGLYCOLATE
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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesMoritella marina (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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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)215,37816
Polymers214,1308
Non-polymers1,2488
Water5,549308
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8444
Polymers53,5322
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-28 kcal/mol
Surface area18410 Å2
MethodPISA
2
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8444
Polymers53,5322
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-28 kcal/mol
Surface area18410 Å2
MethodPISA
3
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8444
Polymers53,5322
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-28 kcal/mol
Surface area18410 Å2
MethodPISA
4
J: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8444
Polymers53,5322
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-28 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.508, 138.076, 89.524
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.006, 0.013, 1), (0.009, 1, -0.013), (-1, 0.009, 0.005)-0.88909, 34.70283, 88.44016
2given(1, -0.009, 0.012), (-0.009, -1, 0.013), (0.012, -0.013, -1)-0.472, 102.19006, 88.85377
3given(-0.017, 1), (-1), (1, 0.017)-0.00501, 67.85617, 0.00322

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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: COMPLEX WITH 2-PHOSPHOGLYCOLATE / Source: (gene. exp.) Moritella marina (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P50921, triose-phosphate isomerase
#2: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 7.5
Details: 100MM TRIETHANOLAMINE/HCL 2.OM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 20MM PGA PH 7.5
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
7100 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / 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: 2.7→25 Å / Num. obs: 59692 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 7 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 332463
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRE
Resolution: 2.7→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 -5 %RANDOM
Rwork0.192 ---
obs0.192 59609 99.9 %-
Displacement parametersBiso mean: 14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 18 77 3828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 -4.7 %
Rwork0.25 6801 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PGA.PARPGA.TOP
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_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor obs: 0.25

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