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- PDB-4a3r: Crystal structure of Enolase from Bacillus subtilis. -

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Basic information

Entry
Database: PDB / ID: 4a3r
TitleCrystal structure of Enolase from Bacillus subtilis.
ComponentsENOLASE
KeywordsLYASE / GLYCOLYSIS / DEGRADOSOME
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / sporulation resulting in formation of a cellular spore / glycolytic process / magnesium ion binding / cell surface / 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
CITRIC ACID / Enolase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNewman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A.S. / Harwood, C.R. / Lewis, R.J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Dissection of the Network of Interactions that Links RNA Processing with Glycolysis in the Bacillus Subtilis Degradosome.
Authors: Newman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A.S. / Harwood, C.R. / Lewis, R.J.
History
DepositionOct 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_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
B: ENOLASE
C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,7437
Polymers186,5054
Non-polymers2383
Water14,196788
1
A: ENOLASE
B: ENOLASE

A: ENOLASE
B: ENOLASE

A: ENOLASE
B: ENOLASE

A: ENOLASE
B: ENOLASE


Theoretical massNumber of molelcules
Total (without water)373,0098
Polymers373,0098
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area24070 Å2
ΔGint-46.4 kcal/mol
Surface area107390 Å2
MethodPISA
2
C: ENOLASE
D: ENOLASE
hetero molecules

C: ENOLASE
D: ENOLASE
hetero molecules

C: ENOLASE
D: ENOLASE
hetero molecules

C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,96220
Polymers373,0098
Non-polymers95212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area27120 Å2
ΔGint-129 kcal/mol
Surface area105040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.074, 187.074, 56.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9466, 0.3225, -0.007375), (0.3225, -0.9466, -0.001068), (-0.007326, -0.001368, -1)
Vector: -0.00329, -0.06473, -6.69889)

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Components

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


Mass: 46626.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37869, phosphopyruvate hydratase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 54 % / Description: NONE
Crystal growDetails: 1.0 M TRI-SODIUM CITRATE 0.1 M, NA CACODYLATE PH 6.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9804
DetectorType: ADSC CCD / Detector: CCD / Date: May 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 96029 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IYX

1iyx


Resolution: 2.2→19.83 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 4530 5 %
Rwork0.1738 --
obs0.176 90492 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.163 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--5.2044 Å20 Å20 Å2
2---5.2044 Å20 Å2
3---10.4088 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13032 0 15 788 13835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813244
X-RAY DIFFRACTIONf_angle_d1.07217929
X-RAY DIFFRACTIONf_dihedral_angle_d14.6934873
X-RAY DIFFRACTIONf_chiral_restr0.072032
X-RAY DIFFRACTIONf_plane_restr0.0042375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.36351110.28952315X-RAY DIFFRACTION74
2.225-2.25110.35691340.25352376X-RAY DIFFRACTION75
2.2511-2.27850.26461220.24692443X-RAY DIFFRACTION78
2.2785-2.30730.29731270.24652492X-RAY DIFFRACTION79
2.3073-2.33760.32831440.23712513X-RAY DIFFRACTION80
2.3376-2.36960.28271240.23612631X-RAY DIFFRACTION83
2.3696-2.40340.29451430.23472747X-RAY DIFFRACTION87
2.4034-2.43920.29321450.22222755X-RAY DIFFRACTION87
2.4392-2.47730.26011380.21662725X-RAY DIFFRACTION87
2.4773-2.51780.28091270.20392859X-RAY DIFFRACTION91
2.5178-2.56110.26361540.20472866X-RAY DIFFRACTION90
2.5611-2.60760.23771710.19632850X-RAY DIFFRACTION92
2.6076-2.65760.23741480.19992942X-RAY DIFFRACTION94
2.6576-2.71180.26411450.23009X-RAY DIFFRACTION95
2.7118-2.77060.24671790.18182940X-RAY DIFFRACTION95
2.7706-2.83480.22771480.18323072X-RAY DIFFRACTION95
2.8348-2.90550.23381630.19033009X-RAY DIFFRACTION97
2.9055-2.98380.2261740.17673033X-RAY DIFFRACTION96
2.9838-3.07130.24011690.17253049X-RAY DIFFRACTION97
3.0713-3.17010.21771500.1723106X-RAY DIFFRACTION97
3.1701-3.28290.21991400.16813094X-RAY DIFFRACTION97
3.2829-3.41370.20821670.1613087X-RAY DIFFRACTION98
3.4137-3.56820.19441460.15163077X-RAY DIFFRACTION97
3.5682-3.75510.19011480.14773098X-RAY DIFFRACTION96
3.7551-3.98860.1741880.1393000X-RAY DIFFRACTION95
3.9886-4.29370.1691680.13142985X-RAY DIFFRACTION94
4.2937-4.72050.15721630.12682986X-RAY DIFFRACTION93
4.7205-5.39150.19041660.14242954X-RAY DIFFRACTION93
5.3915-6.7480.20521660.17152974X-RAY DIFFRACTION92
6.748-19.83060.17461620.15982975X-RAY DIFFRACTION89

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