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- PDB-6nbm: CRYSTAL STRUCTURE OF ENOLASE FROM LEGIONELLA PNEUMOPHILA BOUND TO... -

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Basic information

Entry
Database: PDB / ID: 6nbm
TitleCRYSTAL STRUCTURE OF ENOLASE FROM LEGIONELLA PNEUMOPHILA BOUND TO PHOSPHATE AND MAGNESIUM
ComponentsEnolase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / cell surface / magnesium ion binding / 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 speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF ENOLASE FROM LEGIONELLA PNEUMOPHILA BOUND TO PHOSPHATE AND MAGNESIUM
Authors: Davies, D.R. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E. / Horanyi, P.S.
History
DepositionDec 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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

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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)94,8848
Polymers94,5972
Non-polymers2876
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-62 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.770, 116.770, 142.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 47298.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: eno, C3927_09475 / Plasmid: LEPNA.01024.A.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S6F4U1, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MORPHEUS H3 (50 MM IMIDAZOLE, 50 MM MES PH 6.5, 20 MM L-GLUTAMIC ACID, 20 MM ALANINE, 20 MM GLYCINE, 20 MM LYSINE;, 20 MM SERINE, 20% GLYCEROL, 10% PEG 4000, TRAY 297444H3 PUCK RLK3-10
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2018
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 77934 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.62 % / Biso Wilson estimate: 33.76 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.07 / Num. unique obs: 31590 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXDEV_3318refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NB2

6nb2


Resolution: 1.9→45.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.72
RfactorNum. reflection% reflection
Rfree0.195 4396 6.01 %
Rwork0.161 --
obs0.163 73107 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 0 14 502 6955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.32521210.29492059X-RAY DIFFRACTION85
1.9216-1.94420.31421210.26311945X-RAY DIFFRACTION80
1.9442-1.96790.29211240.22242026X-RAY DIFFRACTION84
1.9679-1.99280.2391460.2062046X-RAY DIFFRACTION86
1.9928-2.01910.22481430.20622105X-RAY DIFFRACTION87
2.0191-2.04670.26211330.20542158X-RAY DIFFRACTION89
2.0467-2.0760.26541380.1972135X-RAY DIFFRACTION89
2.076-2.10690.2481220.19122199X-RAY DIFFRACTION91
2.1069-2.13990.21891420.18362232X-RAY DIFFRACTION91
2.1399-2.1750.23141450.18072233X-RAY DIFFRACTION93
2.175-2.21250.22891470.18342182X-RAY DIFFRACTION91
2.2125-2.25270.25691390.18922258X-RAY DIFFRACTION92
2.2527-2.2960.22251420.17652190X-RAY DIFFRACTION91
2.296-2.34290.20241520.15982305X-RAY DIFFRACTION95
2.3429-2.39380.2191390.16892321X-RAY DIFFRACTION95
2.3938-2.44950.20161440.17152313X-RAY DIFFRACTION96
2.4495-2.51080.19211470.16022369X-RAY DIFFRACTION96
2.5108-2.57860.19611320.16022359X-RAY DIFFRACTION96
2.5786-2.65450.19671730.16392340X-RAY DIFFRACTION97
2.6545-2.74020.2111680.16482339X-RAY DIFFRACTION97
2.7402-2.83810.18041550.15522397X-RAY DIFFRACTION98
2.8381-2.95170.19561560.1652406X-RAY DIFFRACTION98
2.9517-3.0860.17161440.16292415X-RAY DIFFRACTION98
3.086-3.24870.19761700.15772405X-RAY DIFFRACTION98
3.2487-3.45210.20791630.16112426X-RAY DIFFRACTION99
3.4521-3.71860.17591570.14852447X-RAY DIFFRACTION99
3.7186-4.09260.16161520.13232470X-RAY DIFFRACTION99
4.0926-4.68420.13451680.12162484X-RAY DIFFRACTION99
4.6842-5.89960.17721590.14252537X-RAY DIFFRACTION99
5.8996-45.20680.20061540.16212610X-RAY DIFFRACTION97
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)
10.56890.1148-0.24910.98520.0110.70330.23220.16370.3106-0.0395-0.02040.0274-0.8869-0.2803-0.00220.85130.23550.18550.18780.10550.403640.537438.959828.289
22.12280.0808-1.40660.3991-0.10832.1349-0.0360.1043-0.0965-0.0090.0175-0.0273-0.0254-0.07780.01680.2540.03270.0270.12850.00480.218547.926210.483918.0754
30.7215-0.2448-0.15031.05030.53310.27940.12020.3240.2625-0.10620.0479-0.0548-0.6765-0.3283-0.05630.53480.15640.0910.25960.10620.304443.702329.785613.7264
44.0061-1.49760.83192.8228-0.8180.51630.13040.36810.0952-0.20150.03690.1858-0.3874-0.5141-0.11430.37160.18170.06770.33790.07930.246131.217522.206122.5439
51.9113-0.84020.09271.8941-0.55650.2014-0.0306-0.03290.0310.00410.12310.2165-0.3824-0.77970.00240.34310.23180.03850.51450.07780.286620.222817.929639.306
62.0276-0.3387-0.01860.7468-0.21411.55190.0158-0.0550.05270.07450.06910.1016-0.4354-0.3653-0.0330.34150.16710.08390.25940.05130.213433.575420.911448.4134
71.20650.1918-0.05911.2299-0.83692.67020.0573-0.2015-0.10680.08730.0127-0.0006-0.0941-0.0453-0.06040.21080.0830.03430.22720.01860.184742.54739.104260.5662
81.3754-0.4249-0.64671.0338-0.4240.98470.0645-0.23950.2030.14010.0726-0.0075-0.621-0.1952-0.09740.44690.15380.06920.28220.00550.267534.764625.532452.881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 158 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 159 THROUGH 310 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 311 THROUGH 380 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 381 THROUGH 428 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 5 THROUGH 79 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 80 THROUGH 221 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 222 THROUGH 350 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 351 THROUGH 428 )

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