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- PDB-3zlh: Structure of group A Streptococcal enolase -

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Basic information

Entry
Database: PDB / ID: 3zlh
TitleStructure of group A Streptococcal enolase
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
Biological speciesSTREPTOCOCCUS PYOGENES MGAS10394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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


Theoretical massNumber of molelcules
Total (without water)198,3064
Polymers198,3064
Non-polymers00
Water00
1
A: ENOLASE


Theoretical massNumber of molelcules
Total (without water)49,5771
Polymers49,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENOLASE


Theoretical massNumber of molelcules
Total (without water)49,5771
Polymers49,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENOLASE


Theoretical massNumber of molelcules
Total (without water)49,5771
Polymers49,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ENOLASE


Theoretical massNumber of molelcules
Total (without water)49,5771
Polymers49,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)185.795, 185.795, 56.324
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-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 433 / Label seq-ID: 20 - 453

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.06824, 0.9977, -0.005534), (0.9976, 0.06817, -0.01086), (-0.01046, -0.006262, -0.9999)0.1459, 0.2705, 55.06
2given(-0.5043, -0.8635, -0.001344), (-0.8635, 0.5043, -0.003647), (0.003827, -0.000679, -1)-127, -33.39, 28
3given(-0.8267, 0.5627, 0.003711), (-0.5627, -0.8267, 0.005337), (0.006071, 0.002324, 1)-24.57, -129.1, 28.23

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Components

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


Mass: 49576.566 Da / Num. of mol.: 4
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

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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: 2.48 Å3/Da / Density % sol: 50.5 % / 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: 1.072196
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072196 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.545
11K, H, -L20.455
ReflectionResolution: 2.9→19.75 Å / Num. obs: 43076 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 50.855 Å2 / Rmerge(I) obs: 0.43 / Net I/σ(I): 4.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 5 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.91 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W6T

1w6t


Resolution: 2.9→19.75 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.755 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 2185 5.1 %RANDOM
Rwork0.15265 ---
obs0.15528 40890 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.125 Å2
Baniso -1Baniso -2Baniso -3
1--7.63 Å20 Å20 Å2
2---7.63 Å20 Å2
3---15.25 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13172 0 0 0 13172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913381
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212751
X-RAY DIFFRACTIONr_angle_refined_deg1.731.96118085
X-RAY DIFFRACTIONr_angle_other_deg1.359329333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7551710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1224.943617
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.996152295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4531575
X-RAY DIFFRACTIONr_chiral_restr0.090.22028
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215373
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022938
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7744.4576867
X-RAY DIFFRACTIONr_mcbond_other3.7744.4576866
X-RAY DIFFRACTIONr_mcangle_it5.7956.6788568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1274.8396514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A280280.04
12B280280.04
21A272510.06
22C272510.06
31A274520.06
32D274520.06
41B272840.06
42C272840.06
51B275910.06
52D275910.06
61C276240.04
62D276240.04
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 164 -
Rwork0.199 2968 -
obs--98.52 %

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