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- PDB-3zlg: Structure of group A Streptococcal enolase K362A mutant -

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Basic information

Entry
Database: PDB / ID: 3zlg
TitleStructure of group A Streptococcal enolase K362A mutant
ComponentsENOLASE
KeywordsLYASE / PLASMINOGEN-BINDING
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / peptidoglycan-based cell wall / glycolytic process / cell surface / magnesium ion binding / extracellular region / plasma membrane
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
PHOSPHATE ION / Enolase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES MGAS10394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCork, A.J. / Ericsson, D.J. / Law, R.H.P. / Casey, L.W. / Valkov, E. / Bertozzi, C. / Stamp, A. / Aquilina, J.A. / Whisstock, J.C. / Walker, M.J. / Kobe, B.
CitationJournal: Plos One / Year: 2015
Title: Stability of the Octameric Structure Affects Plasminogen-Binding Capacity of Streptococcal Enolase.
Authors: Cork, A.J. / Ericsson, D.J. / Law, R.H.P. / Casey, L.W. / Valkov, E. / Bertozzi, C. / Stamp, A. / Jovcevski, B. / Aquilina, J.A. / Whisstock, J.C. / Walker, M.J. / Kobe, B.
History
DepositionJan 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOLASE
B: ENOLASE
C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,83412
Polymers198,0744
Non-polymers7608
Water7,638424
1
A: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7083
Polymers49,5181
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7083
Polymers49,5181
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7083
Polymers49,5181
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7083
Polymers49,5181
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.255, 187.255, 57.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.8458, -0.5334, 0.00696), (-0.5334, -0.8459, -0.006703), (0.009463, 0.001958, -1)0.1785, -0.1016, -62.84
2given(0.4776, 0.8786, -0.005644), (-0.8786, 0.4776, -0.001648), (0.001247, 0.005745, 1)37.53, 126.7, -30.04
3given(-0.495, 0.8688, -0.01049), (0.8689, 0.495, -0.004663), (0.001142, -0.01142, -0.9999)127.6, -34.94, -33.28

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Components

#1: Protein
ENOLASE / 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE / 2-PHOSPHOGLYCERATE DEHYDRATASE


Mass: 49518.465 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES MGAS10394 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5XD01, phosphopyruvate hydratase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.57 Å3/Da / Density % sol: 52.1 % / Description: NONE
Crystal growpH: 6
Details: 1-3.5 M SODIUM/POTASSIUM PHOSPHATE BUFFER (PH 5-7.5); 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979459
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979459 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.09
ReflectionResolution: 2.1→19.97 Å / Num. obs: 116292 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 29.86 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.16
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W6T

1w6t


Resolution: 2.1→19.969 Å / σ(F): 1.34 / Phase error: 25.35 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.207 5863 5 %
Rwork0.1787 --
obs0.1834 116292 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13240 0 40 424 13704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613484
X-RAY DIFFRACTIONf_angle_d0.92618240
X-RAY DIFFRACTIONf_dihedral_angle_d13.3284924
X-RAY DIFFRACTIONf_chiral_restr0.0512040
X-RAY DIFFRACTIONf_plane_restr0.0042392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13620.29372900.26215462X-RAY DIFFRACTION95
2.1362-2.1750.28673060.24895466X-RAY DIFFRACTION95
2.175-2.21670.27873110.25175445X-RAY DIFFRACTION95
2.2167-2.26190.3922970.35775486X-RAY DIFFRACTION95
2.2619-2.3110.29563110.26995438X-RAY DIFFRACTION95
2.311-2.36460.23923010.2145479X-RAY DIFFRACTION95
2.3646-2.42360.23442790.20765495X-RAY DIFFRACTION95
2.4236-2.4890.23543060.20855502X-RAY DIFFRACTION95
2.489-2.5620.24282930.20455448X-RAY DIFFRACTION95
2.562-2.64450.23362980.20475517X-RAY DIFFRACTION95
2.6445-2.73870.25252910.19695480X-RAY DIFFRACTION95
2.7387-2.84790.22062940.19495538X-RAY DIFFRACTION95
2.8479-2.9770.23163040.19885488X-RAY DIFFRACTION95
2.977-3.13320.22043290.19485453X-RAY DIFFRACTION94
3.1332-3.32830.21972990.19225523X-RAY DIFFRACTION95
3.3283-3.58340.20082330.17055616X-RAY DIFFRACTION96
3.5834-3.94050.1822850.15195523X-RAY DIFFRACTION95
3.9405-4.50280.13672820.12685581X-RAY DIFFRACTION95
4.5028-5.64360.15222800.1355648X-RAY DIFFRACTION95
5.6436-17.93640.18212740.15175766X-RAY DIFFRACTION95
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)
10.613-0.27390.32911.9011-0.25881.63140.06190.1845-0.0582-0.4108-0.0554-0.00910.03080.1452-0.01790.27530.0110.01020.2643-0.03450.21930.77177.0153-43.7509
21.3580.13210.37173.04390.46571.0873-0.05440.0906-0.0083-0.20750.1038-0.7303-0.09430.3994-0.03910.2677-0.0360.02550.3504-0.00160.358952.24356.6665-30.7219
31.36910.4749-0.52241.06480.20791.11280.1185-0.28910.06540.2153-0.10070.00220.04410.0265-0.01710.24050.0075-0.01350.283-0.02180.210122.3878-22.4436-19.0342
41.10580.10920.19480.999-0.1450.63740.0091-0.026-0.134-0.0134-0.0376-0.1860.14890.13150.01750.26090.0840.02450.29380.00720.255340.6596-33.3653-31.7553
51.9377-0.25490.40.49090.13461.21380.07310.3949-0.0394-0.1325-0.0272-0.0442-0.0283-0.0262-0.04650.18910.0070.04330.2767-0.01690.2301101.9515-63.1144-13.3656
61.8809-0.4633-0.10991.4181-0.02151.00010.11330.07760.4836-0.0139-0.0405-0.2414-0.250.1097-0.07220.2587-0.02360.0460.2733-0.01650.3832112.5218-44.4808-0.6093
71.52210.21780.5150.5946-0.15211.28130.0707-0.315-0.09310.1398-0.01910.0508-0.0374-0.0868-0.05940.17820.00860.05260.23910.01880.218484.4272-63.2811.2888
81.77320.1122-0.36721.2784-0.14231.19850.1184-0.01870.38950.0456-0.04450.0838-0.2744-0.0648-0.0720.26580.03130.04680.25210.00720.328273.418-44.8549-1.9667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 151 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 152 THROUGH 433 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 1 THROUGH 151 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 152 THROUGH 433 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 1 THROUGH 151 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 152 THROUGH 433 )
7X-RAY DIFFRACTION7CHAIN D AND (RESID 1 THROUGH 151 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 152 THROUGH 433 )

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