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- PDB-3zlf: Structure of group A Streptococcal enolase K312A mutant -

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Basic information

Entry
Database: PDB / ID: 3zlf
TitleStructure of group A Streptococcal enolase K312A 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 / magnesium ion binding / cell surface / 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: 2.15 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

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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
Water10,395577
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)181.620, 181.620, 56.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:433 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
211CHAIN C AND NOT (RESSEQ 39:46 OR RESSEQ 154:155 OR...
311CHAIN D AND NOT (RESSEQ 39:66 OR RESSEQ 154:156 OR...

NCS oper:
IDCodeMatrixVector
1given(0.02659, 0.9993, -0.02579), (0.9992, -0.02737, -0.03059), (-0.03128, -0.02496, -0.9992)-2.196, 2.184, 3.992
2given(-0.4979, -0.8669, 0.02228), (-0.8671, 0.4982, 0.005963), (-0.01627, -0.01635, -0.9997)91.22, 90.87, -23.57
3given(-0.8757, 0.4822, 0.02406), (-0.4822, -0.876, 0.006425), (0.02418, -0.005978, 0.9997)91.35, 90.95, 23.41

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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.: 577 / 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: 2.38 Å3/Da / Density % sol: 48.3 % / 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: 0.14
ReflectionResolution: 2.15→90.81 Å / Num. obs: 100879 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 10.64
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 2.13 / % 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: 2.15→90.81 Å / σ(F): 1.34 / Phase error: 23.66 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1991 5064 5 %
Rwork0.1725 --
obs0.1763 100879 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.9 Å2
Refinement stepCycle: LAST / Resolution: 2.15→90.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13302 0 40 577 13919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513549
X-RAY DIFFRACTIONf_angle_d0.86618325
X-RAY DIFFRACTIONf_dihedral_angle_d13.3714949
X-RAY DIFFRACTIONf_chiral_restr0.0462047
X-RAY DIFFRACTIONf_plane_restr0.0032402
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2891X-RAY DIFFRACTIONPOSITIONAL
12C2891X-RAY DIFFRACTIONPOSITIONAL0.025
13D2672X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18710.25742600.24664753X-RAY DIFFRACTION95
2.1871-2.22690.27212470.2384778X-RAY DIFFRACTION95
2.2269-2.26970.27292680.23364730X-RAY DIFFRACTION95
2.2697-2.3160.27252420.22834744X-RAY DIFFRACTION95
2.316-2.36640.2572580.21824745X-RAY DIFFRACTION95
2.3664-2.42140.24082450.21474752X-RAY DIFFRACTION95
2.4214-2.4820.262540.20694788X-RAY DIFFRACTION95
2.482-2.54910.22852570.20784747X-RAY DIFFRACTION95
2.5491-2.62410.22532410.19984752X-RAY DIFFRACTION95
2.6241-2.70880.2312600.19854791X-RAY DIFFRACTION95
2.7088-2.80570.20892570.19294756X-RAY DIFFRACTION95
2.8057-2.9180.22182310.18954778X-RAY DIFFRACTION95
2.918-3.05080.23532370.18864789X-RAY DIFFRACTION95
3.0508-3.21170.22892560.18924774X-RAY DIFFRACTION95
3.2117-3.41290.23032300.17654834X-RAY DIFFRACTION95
3.4129-3.67640.18262690.16044782X-RAY DIFFRACTION95
3.6764-4.04640.16362510.14294847X-RAY DIFFRACTION95
4.0464-4.63190.15092380.12984830X-RAY DIFFRACTION95
4.6319-5.83550.15062710.13524848X-RAY DIFFRACTION95
5.8355-90.89110.15522920.15194995X-RAY DIFFRACTION94
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)
10.2233-0.0047-0.19370.5751-0.00440.2-0.0040.06060.04750.26290.0061-0.0967-0.0730.00580.01430.2379-0.0039-0.01660.12680.00530.111360.459883.975416.4511
20.0666-0.0122-0.02280.4745-0.01290.2910.00120.0763-0.0943-0.12310.00570.1251-0.0430.0419-0.00120.19440.0106-0.05090.15190.00620.262747.145678.9782-6.0081
30.320.07870.12440.35830.02910.04460.03950.0294-0.0332-0.05540.02310.4874-0.07530.0119-0.0010.20280.0041-0.01290.21390.00420.462631.09472.53290.6135
40.1037-0.1689-0.01920.3998-0.10630.08670.00240.0364-0.0903-0.0651-0.00030.1468-0.0660.0801-0.01180.1617-0.002-0.00970.1563-0.00820.239548.918868.92731.454
50.5961-0.0317-0.04070.06740.08260.07310.04510.32890.0831-0.0208-0.0155-0.0446-0.0006-0.03-0.00150.20760.0156-0.01410.3149-0.00390.152683.315460.5501-16.5939
60.52720.06780.0290.0644-0.03170.01040.016-0.0386-0.07620.0763-0.0333-0.0241-0.04370.0692-0.00050.20860.00860.00830.2263-0.00270.203878.295347.46596.2612
70.2730.09420.0590.2352-0.12690.10970.0114-0.0236-0.27750.0275-0.10470.0220.07070.0474-0.0050.2617-0.0013-0.00160.2007-0.03940.426770.842430.93050.661
80.42230.03810.0570.18010.11680.04890.00650.0519-0.04430.0182-0.00850.021-0.12310.01430.00090.17230.0133-0.01320.2214-0.01810.186468.294149.1947-1.0703
90.377-0.19860.01570.227-0.1250.0940.03170.0735-0.07140.04660.00410.046-0.05180.05290.02660.1761-0.0111-0.00820.2015-0.00610.048320.661422.586-40.7455
100.0838-0.0107-0.00760.0195-0.02570.09350.1136-0.0879-0.01520.077-0.09920.08150.0146-0.00490.00620.2222-0.01420.00690.2348-0.00550.151728.684923.344-22.8689
110.2472-0.1062-0.11860.17790.03280.1668-0.0609-0.19720.0003-0.0129-0.00470.05320.00080.0488-0.06830.2253-0.0262-0.02880.2289-0.01680.129334.975439.8716-14.3679
120.12730.0641-0.01970.14780.0830.077-0.07190.04230.0753-0.02690.0848-0.0364-0.05630.0684-00.2843-0.06170.00180.29320.0060.197245.429442.565-25.6315
130.1649-0.1083-0.06020.08480.01530.0525-0.019-0.02010.03270.04440.0117-0.05430.0037-0.046-0.04020.1697-0.0339-0.00690.1937-0.00690.107239.619125.3623-26.1835
140.08620.2113-0.04910.4777-0.10870.10520.0393-0.02280.06690.1414-0.04380.03330.01770.0420.00290.2633-0.0022-0.00750.2463-0.00390.139430.1986-8.7729-7.7662
150.06680.0852-0.0620.1066-0.09480.0896-0.0003-0.0102-0.00120.0549-0.0222-0.1280.03220.0223-00.21650.015-0.00030.22780.01320.216336.9072-5.1891-25.7523
160.05760.0495-0.08331.22160.1660.1199-0.005-0.01950.04930.10460.01-0.33940.01680.05990.00050.17490.0137-0.02620.26160.01730.219751.6142-6.677-25.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 0 THROUGH 119 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 120 THROUGH 199 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 200 THROUGH 279 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 280 THROUGH 435 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 0 THROUGH 119 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 120 THROUGH 199 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 200 THROUGH 279 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 280 THROUGH 433 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 0 THROUGH 119 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 120 THROUGH 159 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 160 THROUGH 199 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 200 THROUGH 279 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 280 THROUGH 434 )
14X-RAY DIFFRACTION14CHAIN D AND (RESID 0 THROUGH 119 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 120 THROUGH 159 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 160 THROUGH 433 )

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