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- PDB-2psn: Crystal structure of enolase1 -

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Basic information

Entry
Database: PDB / ID: 2psn
TitleCrystal structure of enolase1
ComponentsAlpha-enolase
KeywordsLYASE / Enolase1
Function / homology
Function and homology information


negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / nuclear outer membrane / M band ...negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / nuclear outer membrane / M band / canonical glycolysis / Glycolysis / positive regulation of ATP biosynthetic process / transcription corepressor binding / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / glycolytic process / response to virus / negative regulation of cell growth / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / GTPase binding / cell cortex / cadherin binding / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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 / Alpha-enolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHyo, J.K. / Seung, J.K. / Sang, J.C.
CitationJournal: To be Published
Title: Crystal Structure of Enolase1 alpha
Authors: Hyo, J.K. / Seung, J.K. / Sang, J.C. / Suk-Kyeong, J.
History
DepositionMay 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.value / _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_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: Alpha-enolase
B: Alpha-enolase
C: Alpha-enolase
D: Alpha-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,49416
Polymers188,9194
Non-polymers57412
Water10,701594
1
A: Alpha-enolase
B: Alpha-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7478
Polymers94,4602
Non-polymers2876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-66 kcal/mol
Surface area27960 Å2
MethodPISA, PQS
2
C: Alpha-enolase
D: Alpha-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7478
Polymers94,4602
Non-polymers2876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-68 kcal/mol
Surface area27880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)192.796, 192.796, 65.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
Alpha-enolase / / 2-phospho-D-glycerate hydro-lyase / Non-neural enolase / NNE / Enolase 1 / Phosphopyruvate ...2-phospho-D-glycerate hydro-lyase / Non-neural enolase / NNE / Enolase 1 / Phosphopyruvate hydratase / C-myc promoter-binding protein / MBP-1 / MPB-1 / Plasminogen-binding protein


Mass: 47229.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This sequence occurs naturally in humans. / Source: (gene. exp.) Homo sapiens (human) / Gene: ENO1, ENO1L1, MBPB1, MPB1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P06733, phosphopyruvate hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% to 24% (w/v) PEG 3350, 100 mM Tris-HCl (pH 7.5), 200 mM ammoniumsulfate, 1 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 6, 2006 / Details: mirror
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 120965 / Num. obs: 121573 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.1 / Num. unique all: 11810 / Rsym value: 0.239 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS0.9refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5969 -random
Rwork0.184 ---
obs0.184 118254 96.8 %-
all-122136 --
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13193 0 28 594 13815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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