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- PDB-2xsx: Crystal structure of human beta enolase ENOB -

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Basic information

Entry
Database: PDB / ID: 2xsx
TitleCrystal structure of human beta enolase ENOB
ComponentsBETA-ENOLASE
KeywordsLYASE
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / glycolytic process / gluconeogenesis / magnesium ion binding / extracellular space ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / glycolytic process / gluconeogenesis / magnesium ion binding / extracellular space / extracellular exosome / 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
PHOSPHATE ION / Beta-enolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVollmar, M. / Krysztofinska, E. / Chaikuad, A. / Krojer, T. / Cocking, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Vollmar, M. / Krysztofinska, E. / Chaikuad, A. / Krojer, T. / Cocking, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Beta Enolase Enob
Authors: Vollmar, M. / Krysztofinska, E. / Chaikuad, A. / Krojer, T. / Cocking, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Oppermann, U.
History
DepositionSep 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-ENOLASE
B: BETA-ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,57725
Polymers94,1602
Non-polymers1,41823
Water19,5101083
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint15.6 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.878, 105.531, 106.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-ENOLASE / 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE / MUSCLE-SPECIFIC ENOLASE / MSE / SKELETAL MUSCLE ENOLASE / ENOLASE 3


Mass: 47079.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P13929, phosphopyruvate hydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / 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: 2.65 Å3/Da / Density % sol: 53.62 % / Description: NONE
Crystal growDetails: 0.1M NA_ACETATE, 25% PEG_8000, 0.1M CACODYLATE PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9245
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9245 Å / Relative weight: 1
ReflectionResolution: 1.7→29.49 Å / Num. obs: 114102 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.1 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TE6, 2AKM, 2AKZ, 2PSN AND 3B97

1te6

2akm

2akz

2psn

3b97


Resolution: 1.7→29.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.238 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. DISORDERED LOOP BETWEEN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. DISORDERED LOOP BETWEEN RESIDUES 37 AND 43 IN BOTH MOLECULES WHICH IS PROBABLY DUE TO MULTIPLE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18905 5697 5 %RANDOM
Rwork0.15282 ---
obs0.15463 108327 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.721 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--1.24 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 88 1083 7763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226896
X-RAY DIFFRACTIONr_bond_other_d0.0010.024753
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9789263
X-RAY DIFFRACTIONr_angle_other_deg2.069311683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33125.087289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6471534
X-RAY DIFFRACTIONr_chiral_restr0.0910.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021289
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_it2.54454355
X-RAY DIFFRACTIONr_mcbond_other1.10351812
X-RAY DIFFRACTIONr_mcangle_it3.09476965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.33992541
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.422112298
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
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 400 -
Rwork0.211 7640 -
obs--92.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88140.12611.05491.2125-0.68692.95170.0782-0.0302-0.1226-0.0209-0.00490.17640.0836-0.1708-0.07330.0415-0.0064-0.02440.03050.00820.0627-29.8823-7.5787-1.0624
20.72060.17990.25720.94180.14090.56750.0720.0034-0.0607-0.0132-0.05470.05170.0431-0.0561-0.01730.01830.0111-0.00610.0227-0.00140.0107-28.368910.5334-5.8702
318.17193.410611.81394.476-0.12729.1136-0.1294-0.52460.11281.00770.34690.6195-0.7726-0.5633-0.21750.28770.10470.16220.11150.04570.0953-38.53925.204316.6694
41.1097-0.2055-0.14491.07010.34350.86810.03420.0304-0.0434-0.0056-0.02050.1413-0.0184-0.1186-0.01370.0050.0034-0.00180.01720.00550.0244-34.857417.1015-4.4135
50.5406-0.634-0.21152.8437-0.18160.97110.09180.2064-0.0669-0.2534-0.1057-0.14310.10860.15530.01380.09630.0770.01470.1802-0.0510.0473-4.7938-1.2361-21.4084
61.0550.24970.03460.838-0.03260.87970.0175-0.0147-0.07520.0547-0.0541-0.08810.00740.12030.03670.01840.0083-0.00370.04170.02190.02050.45491.019611.2478
75.4788-1.49224.2073.5384-0.727.79350.14440.8923-0.055-0.2377-0.3398-0.44090.16280.93050.19540.07670.0880.0470.26390.00810.110915.59-5.2702-5.8632
81.8735-0.1557-0.04090.83070.04580.9640.00310.1583-0.1912-0.052-0.028-0.0720.2080.12940.02480.08110.0506-0.00420.045-0.02060.0367-4.1786-10.0874-4.3169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 67
2X-RAY DIFFRACTION2A68 - 253
3X-RAY DIFFRACTION3A254 - 258
4X-RAY DIFFRACTION4A259 - 434
5X-RAY DIFFRACTION5B1 - 144
6X-RAY DIFFRACTION6B145 - 319
7X-RAY DIFFRACTION7B320 - 336
8X-RAY DIFFRACTION8B337 - 434

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