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- PDB-3ucc: Asymmetric complex of human neuron specific enolase-1-PGA/PEP -

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Basic information

Entry
Database: PDB / ID: 3ucc
TitleAsymmetric complex of human neuron specific enolase-1-PGA/PEP
ComponentsGamma-enolase
KeywordsLYASE
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / synaptic membrane / glycolytic process / gluconeogenesis ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / synaptic membrane / glycolytic process / gluconeogenesis / response to estradiol / growth cone / cell cortex / perikaryon / membrane raft / response to xenobiotic stimulus / protein-containing complex binding / enzyme binding / magnesium ion binding / cell surface / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol
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
2-PHOSPHOGLYCERIC ACID / Gamma-enolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsQin, J. / Chai, G. / Brewer, J. / Lovelace, L. / Lebioda, L.
CitationJournal: J.Inorg.Biochem. / Year: 2012
Title: Structures of asymmetric complexes of human neuron specific enolase with resolved substrate and product and an analogous complex with two inhibitors indicate subunit interaction and inhibitor cooperativity.
Authors: Qin, J. / Chai, G. / Brewer, J.M. / Lovelace, L.L. / Lebioda, L.
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_ref_seq_dif.details / _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: Gamma-enolase
B: Gamma-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6269
Polymers96,0342
Non-polymers5917
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-52 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.785, 119.677, 68.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-443-

HOH

21B-483-

HOH

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Components

#1: Protein Gamma-enolase / 2-phospho-D-glycerate hydro-lyase / Enolase 2 / Neural enolase / Neuron-specific enolase / NSE


Mass: 48017.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P09104, phosphopyruvate hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG4K, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 131445 / % possible obs: 87.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.084 / Χ2: 3.407 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.551.60.34762001.294141.7
1.55-1.622.20.3995281.124164
1.62-1.692.80.376123801.186183.4
1.69-1.783.70.367131881.271188.7
1.78-1.894.80.326144631.481196.7
1.89-2.045.90.252148781.944199.8
2.04-2.246.30.163150012.8081100
2.24-2.566.60.109150443.4941100
2.56-3.237.10.078151614.8651100
3.23-507.20.047156026.299199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIguidata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AKM

2akm


Resolution: 1.5→36.44 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.862 / WRfactor Rfree: 0.2329 / WRfactor Rwork: 0.1999 / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.884 / SU B: 3.76 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1322 / SU Rfree: 0.1037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 6211 5 %RANDOM
Rwork0.2197 ---
obs0.2216 124405 82.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 234.17 Å2 / Biso mean: 7.5783 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 34 601 7255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226757
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9729142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39825308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.335151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7951540
X-RAY DIFFRACTIONr_chiral_restr0.1340.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215112
X-RAY DIFFRACTIONr_mcbond_it1.4261.54279
X-RAY DIFFRACTIONr_mcangle_it2.27826842
X-RAY DIFFRACTIONr_scbond_it3.89632478
X-RAY DIFFRACTIONr_scangle_it5.9474.52300
X-RAY DIFFRACTIONr_rigid_bond_restr2.22436757
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 184 -
Rwork0.277 3470 -
all-3654 -
obs--33.24 %

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