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- PDB-4mva: 1.43 Angstrom Resolution Crystal Structure of Triosephosphate Iso... -

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Basic information

Entry
Database: PDB / ID: 4mva
Title1.43 Angstrom Resolution Crystal Structure of Triosephosphate Isomerase (tpiA) from Escherichia coli in Complex with Acetyl Phosphate.
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 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / ACETYLPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMinasov, G. / Kuhn, M.L. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Grimshaw, S. / Kwon, K. / 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
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / 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 / _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)60,1369
Polymers59,4952
Non-polymers6417
Water15,079837
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-26 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.535, 67.529, 150.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: BWG_3588, tpiA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: C5A086, triose-phosphate isomerase

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Non-polymers , 6 types, 844 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UVW / ACETYLPHOSPHATE


Mass: 140.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O5P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7.4mg/mL, 0.15M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 10mM ACP, VAPOR DIFFUSION, SITTING ...Details: Protein: 7.4mg/mL, 0.15M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 10mM ACP, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.43→30 Å / Num. all: 88659 / Num. obs: 88659 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.7
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4416 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRE

1tre


Resolution: 1.43→29.24 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.842 / SU ML: 0.037
Isotropic thermal model: Thermal Factors Isotropically Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15614 4433 5 %RANDOM
Rwork0.13456 ---
all0.13567 83946 --
obs0.13567 83946 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.023 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0 Å2
2--0.66 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.43→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 37 837 4654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194429
X-RAY DIFFRACTIONr_bond_other_d0.0010.024304
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9566035
X-RAY DIFFRACTIONr_angle_other_deg0.76239947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5885616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62325.543184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.70115779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2421520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.025319
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02961
X-RAY DIFFRACTIONr_mcbond_it1.2611.212344
X-RAY DIFFRACTIONr_mcbond_other1.2581.2082343
X-RAY DIFFRACTIONr_mcangle_it2.0431.8093000
X-RAY DIFFRACTIONr_mcangle_other2.0441.8113001
X-RAY DIFFRACTIONr_scbond_it2.0841.4562085
X-RAY DIFFRACTIONr_scbond_other2.0841.4562085
X-RAY DIFFRACTIONr_scangle_other3.1292.0823036
X-RAY DIFFRACTIONr_long_range_B_refined6.98812.8965831
X-RAY DIFFRACTIONr_long_range_B_other6.38410.665178
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 326 -
Rwork0.192 6138 -
obs--99.98 %
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)
10.29280.2313-0.09670.58390.0440.2895-0.0038-0.0404-0.00630.01860.0180.01150.04770.0026-0.01420.01750.0027-0.00950.01710.00060.01442.1178-22.751717.8125
20.6055-0.1188-0.18560.66080.07540.7388-0.0045-0.0574-0.0720.06850.02930.01580.1525-0.0278-0.02480.0541-0.0051-0.00370.00980.01170.0158-0.7196-35.876423.8375
30.50840.1259-0.06230.73930.18410.3143-0.0008-0.03080.0211-0.03940.04580.0024-0.01680.0383-0.0450.00970.00090.00140.0111-0.00670.011714.46-2.860814.5349
41.0619-0.25770.48570.88040.07150.7399-0.0475-0.05180.11230.0180.0463-0.0826-0.13110.10150.00130.0485-0.01490.0170.0409-0.01960.055322.18269.053218.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2A143 - 254
3X-RAY DIFFRACTION3B1 - 142
4X-RAY DIFFRACTION4B143 - 255

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