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- PDB-5boe: Crystal structure of Staphylococcus aureus enolase in complex with PEP -

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Basic information

Entry
Database: PDB / ID: 5boe
TitleCrystal structure of Staphylococcus aureus enolase in complex with PEP
ComponentsEnolase
KeywordsLYASE / enolase / PEP
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / cell surface / magnesium ion binding / extracellular region
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
PHOSPHOENOLPYRUVATE / Enolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, C.L. / Wu, Y.F. / Han, L. / Wu, M.H. / Zhang, X. / Zang, J.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Octameric structure of Staphylococcus aureus enolase in complex with phosphoenolpyruvate
Authors: Wu, Y. / Wang, C. / Lin, S. / Wu, M. / Han, L. / Tian, C. / Zhang, X. / Zang, J.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Nov 8, 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_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1279
Polymers96,4662
Non-polymers6617
Water11,908661
1
A: Enolase
B: Enolase
hetero molecules

A: Enolase
B: Enolase
hetero molecules

A: Enolase
B: Enolase
hetero molecules

A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,50636
Polymers385,8638
Non-polymers2,64428
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area31760 Å2
ΔGint-170 kcal/mol
Surface area103830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.154, 145.154, 100.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 1 - 433 / Label seq-ID: 1 - 433

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase / Laminin-binding protein


Mass: 48232.820 Da / Num. of mol.: 2 / Mutation: Q197K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: eno / Production host: Escherichia coli (E. coli) / References: UniProt: O69174, phosphopyruvate hydratase
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M Ammonium acetate, 0.1M Tris pH 8.5, 25%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 136548 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BOF

5bof


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.08 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16356 6858 5 %RANDOM
Rwork0.14848 ---
obs0.14923 129690 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2---0.22 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 40 661 7259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197029
X-RAY DIFFRACTIONr_bond_other_d0.0050.026582
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9669574
X-RAY DIFFRACTIONr_angle_other_deg1.047315195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95825.591313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.967151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1771530
X-RAY DIFFRACTIONr_chiral_restr0.0820.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028275
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021519
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_it0.9451.443662
X-RAY DIFFRACTIONr_mcbond_other0.9361.4393661
X-RAY DIFFRACTIONr_mcangle_it1.5062.1574622
X-RAY DIFFRACTIONr_mcangle_other1.5062.1574623
X-RAY DIFFRACTIONr_scbond_it1.571.6283367
X-RAY DIFFRACTIONr_scbond_other1.5691.6283367
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4092.3744948
X-RAY DIFFRACTIONr_long_range_B_refined4.64612.7718767
X-RAY DIFFRACTIONr_long_range_B_other4.52612.5618606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27672 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.602→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 486 -
Rwork0.179 9579 -
obs--99.54 %

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