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- PDB-4g7f: Crystal Structure of Enolase from Trypanosoma Cruzi -

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Basic information

Entry
Database: PDB / ID: 4g7f
TitleCrystal Structure of Enolase from Trypanosoma Cruzi
ComponentsEnolase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Enolase
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphopyruvate hydratase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsCraig, T.K. / Edwards, T.E. / Staker, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Enolase from Trypanosoma Cruzi
Authors: Craig, T.K. / Edwards, T.E. / Staker, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5873
Polymers46,5011
Non-polymers862
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.290, 119.310, 110.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21A-661-

HOH

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Components

#1: Protein Enolase


Mass: 46500.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053504105.140 / Plasmid: TrcrA.01024.a.B1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DZ98, phosphopyruvate hydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 289 K / pH: 8.5
Details: TrcrA.01024.a.B1 PW35751 CR_27 47.62mg/ml Morpheus E12 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each ethylene glycol 0.1 M bicine/Trizma base pH 8.5, VAPOR DIFFUSION, ...Details: TrcrA.01024.a.B1 PW35751 CR_27 47.62mg/ml Morpheus E12 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each ethylene glycol 0.1 M bicine/Trizma base pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9774
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: ASYMMETRIC CURVED CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19797 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 47.061 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.74
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.89 Å19.81 Å
Translation4.89 Å19.81 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OEP

1oep


Resolution: 2.4→19.809 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.36 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 993 5.02 %
Rwork0.1892 --
obs0.1923 19774 99.96 %
all-19857 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.8464 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 5 89 3091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143058
X-RAY DIFFRACTIONf_angle_d1.4674159
X-RAY DIFFRACTIONf_dihedral_angle_d14.3811065
X-RAY DIFFRACTIONf_chiral_restr0.078483
X-RAY DIFFRACTIONf_plane_restr0.007554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52630.30251430.21812663X-RAY DIFFRACTION100
2.5263-2.68420.28791390.21842631X-RAY DIFFRACTION100
2.6842-2.89090.27191340.21642653X-RAY DIFFRACTION100
2.8909-3.18080.24671510.21162669X-RAY DIFFRACTION100
3.1808-3.63860.25921410.20012655X-RAY DIFFRACTION100
3.6386-4.57490.22841400.16392707X-RAY DIFFRACTION100
4.5749-19.80990.2391450.17532803X-RAY DIFFRACTION100
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)
13.1191.42730.8745.50472.47863.8459-0.26110.03350.15710.10430.23460.35140.0371-0.2869-0.03080.15860.030.04060.20990.03620.1359-38.4471-8.4895-14.87
22.96450.5629-0.15132.78960.04813.7099-0.0781-0.2643-0.14530.2212-0.0439-0.08610.29490.02850.09860.2257-0.01750.00160.2398-0.00370.1275-35.5969-10.4902-9.1192
32.10140.1766-0.09522.7548-1.02297.4325-0.0301-0.18460.04170.2197-0.0040.10680.22090.63490.09950.14070.01480.03080.222-0.01330.183-27.1884-5.6045-8.9338
41.194-1.44540.05584.95952.45322.1070.26010.2910.0832-0.0213-0.188-0.26840.22130.67620.02670.27370.0740.01440.46330.03180.2093-19.6382-10.2844-27.7349
50.8363-0.9640.03012.3833-0.11440.509-0.02020.0352-0.4471-0.0389-0.03610.00661.03650.40810.06010.78990.18660.06280.33-0.00750.4056-26.6338-33.3115-32.478
60.2801-0.2196-0.2650.80261.48342.8289-0.03850.0509-0.27180.1176-0.0345-0.04241.02010.31880.14730.8440.36370.08540.5617-0.05890.4651-19.1154-33.5538-33.275
70.72890.31080.26041.9548-1.03940.98280.0318-0.2497-0.59890.60820.063-0.16780.0740.0441-0.03661.05070.5368-0.09880.72460.1770.8257-12.3809-42.1104-16.6692
81.49-0.7844-0.62540.93920.67520.5535-0.2317-0.3692-0.33920.1551-0.012-0.01290.46350.4806-0.07140.6260.49530.0350.83770.06880.4336-10.8935-28.011-16.011
90.4271-0.1422-0.35311.19850.01250.3038-0.0864-0.0951-0.21090.09570.0232-0.1570.45860.5905-0.00020.31450.16880.04440.43780.01770.2647-20.3535-16.6955-20.2911
104.1676-2.69930.27343.17750.45010.29110.09260.19110.1624-0.1599-0.0788-0.37640.06240.6293-0.0410.23280.09660.07270.49530.01770.2462-21.6506-12.737-34.5899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 152 )
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 220 )
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 249 )
7X-RAY DIFFRACTION7chain 'A' and (resid 250 through 284 )
8X-RAY DIFFRACTION8chain 'A' and (resid 285 through 333 )
9X-RAY DIFFRACTION9chain 'A' and (resid 334 through 403 )
10X-RAY DIFFRACTION10chain 'A' and (resid 404 through 429 )

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