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- PDB-3tqp: Structure of an enolase (eno) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tqp
TitleStructure of an enolase (eno) from Coxiella burnetii
ComponentsEnolase
KeywordsLYASE / Energy metabolism
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 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
PHOSPHATE ION / Enolase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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.pdbx_leaving_atom_flag / _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: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3316
Polymers94,0932
Non-polymers2394
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-43 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.807, 95.523, 160.743
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47046.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: eno, CBU_1674 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83B44, phosphopyruvate hydratase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293 K / pH: 7
Details: 40% PEG 400, 7% PEG 3000, 100 mM Tris pH 7.0, 30 mM NaOH, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 59163 / Num. obs: 58927 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.081 / Χ2: 1.752 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.11-2.156.80.65326521.592192.2
2.15-2.197.40.49329481.5691100
2.19-2.237.40.45929101.611100
2.23-2.277.40.39229101.7041100
2.27-2.327.40.32129111.6661100
2.32-2.387.40.27829191.6621100
2.38-2.447.40.24429151.7341100
2.44-2.57.40.21429271.8121100
2.5-2.587.40.18129381.8891100
2.58-2.667.40.14629321.8351100
2.66-2.757.40.12329481.5811100
2.75-2.867.30.10629241.6441100
2.86-2.997.30.0929571.6271100
2.99-3.157.20.07829521.6371100
3.15-3.357.20.06629581.8371100
3.35-3.618.90.0929951.8741100
3.61-3.97140.10229752.0951100
3.97-4.5413.50.07729961.8611100
4.54-5.7213.20.06630481.9041100
5.72-5011.90.05432121.469199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.783 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8368 / SU ML: 0.26 / σ(F): 0 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 2614 5.08 %Random
Rwork0.1835 ---
all0.1853 54035 --
obs0.1853 51421 99.87 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.042 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 314.41 Å2 / Biso mean: 53.8215 Å2 / Biso min: 16.95 Å2
Baniso -1Baniso -2Baniso -3
1--4.2829 Å20 Å20 Å2
2--1.8 Å20 Å2
3---2.4829 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 0 12 198 6514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056414
X-RAY DIFFRACTIONf_angle_d0.8778693
X-RAY DIFFRACTIONf_chiral_restr0.061995
X-RAY DIFFRACTIONf_plane_restr0.0031150
X-RAY DIFFRACTIONf_dihedral_angle_d14.082371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.27860.27892510.208548285079
2.2786-2.36990.26232380.192948285066
2.3699-2.47770.25912700.199548095079
2.4777-2.60830.27452340.194648485082
2.6083-2.77170.23752610.191148335094
2.7717-2.98570.26132570.204648715128
2.9857-3.28610.2652620.2148795141
3.2861-3.76140.22322500.187248815131
3.7614-4.73820.17243050.150748925197
4.7382-45.79310.19882860.180451385424
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)
10.6470.69480.4011.2246-0.3181.0735-0.02040.00890.2569-0.11880.15550.4627-0.0463-0.159-0.09250.16390.0228-0.01450.28770.10290.34288.752542.702458.7726
21.11570.31850.6261.60160.31691.4413-0.0444-0.06040.0027-0.12340.18010.63370.0437-0.4921-0.12510.1566-0.0331-0.01530.33260.15080.34675.783935.434159.953
31.2012-0.124-0.81141.9743-0.80641.3623-0.2690.463-0.10570.0105-0.2069-0.27050.02450.08430.31250.1641-0.057-0.03680.42090.13240.262236.076236.890870.2189
42.87360.57841.18991.34520.04561.0440.01950.6279-0.2143-0.1478-0.0489-0.36660.10120.57280.07090.23950.07950.03640.48690.08650.288937.333721.824367.3311
50.6254-0.15090.03972.1242-0.20560.9231-0.0029-0.07510.04360.1050.04390.1607-0.0049-0.125-0.04880.1544-0.00580.03350.28710.09460.182820.555330.973272.5057
62.82450.3760.41440.8286-0.56712.0610.0806-0.27230.54670.3955-0.1218-0.073-0.7701-0.1180.02370.54590.0528-0.01370.2522-0.0450.447224.382964.262271.5711
72.55940.0173-1.32891.41020.12050.5304-0.76060.6312-0.46430.39070.54460.08340.2557-0.05040.18650.37490.0052-0.0620.23670.17230.434325.826456.442247.0981
82.13721.5311-1.09035.8968-0.08351.1538-0.36010.211-0.3358-0.54730.363-1.12530.21010.03340.02710.42120.00180.10040.34110.03280.442433.443548.053841.8023
97.5955-2.31230.13591.91861.43581.9170.2569-1.69291.5637-0.2171-0.1641-0.26090.22720.1905-0.28880.4520.10740.40060.7229-0.05981.087252.688259.432744.0607
102.17481.0122-0.11883.4080.3021.2848-0.18670.10070.3045-0.35190.2256-0.4507-0.42950.0148-0.0590.349-0.03070.03060.20190.13510.400431.001864.354647.639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:46)A2 - 46
2X-RAY DIFFRACTION2(chain A and resid 47:138)A47 - 138
3X-RAY DIFFRACTION3(chain A and resid 139:201)A139 - 201
4X-RAY DIFFRACTION4(chain A and resid 202:306)A202 - 306
5X-RAY DIFFRACTION5(chain A and resid 307:426)A307 - 426
6X-RAY DIFFRACTION6(chain B and resid 2:138)B2 - 138
7X-RAY DIFFRACTION7(chain B and resid 139:160)B139 - 160
8X-RAY DIFFRACTION8(chain B and resid 164:251)B164 - 251
9X-RAY DIFFRACTION9(chain B and resid 254:260)B254 - 260
10X-RAY DIFFRACTION10(chain B and resid 261:425)B261 - 425

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