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- PDB-3qn3: Phosphopyruvate hydratase from Campylobacter jejuni. -

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Basic information

Entry
Database: PDB / ID: 3qn3
TitlePhosphopyruvate hydratase from Campylobacter jejuni.
ComponentsEnolase
KeywordsLYASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / enolase / glycolysis
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
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsOsipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Phosphopyruvate hydratase from Campylobacter jejuni.
Authors: Osipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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: Enolase
B: Enolase
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,16318
Polymers181,0284
Non-polymers1,13414
Water13,962775
1
A: Enolase
B: Enolase
C: Enolase
D: Enolase
hetero molecules

A: Enolase
B: Enolase
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,32536
Polymers362,0578
Non-polymers2,26928
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area29170 Å2
ΔGint-295 kcal/mol
Surface area105740 Å2
MethodPISA
2
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9878
Polymers90,5142
Non-polymers4736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-60 kcal/mol
Surface area29160 Å2
MethodPISA
3
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,17510
Polymers90,5142
Non-polymers6618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-77 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.470, 148.886, 234.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 45257.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: subsp. jejuni NCTC 11168 / Gene: Cj1672c, eno / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42448, phosphopyruvate hydratase

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Non-polymers , 5 types, 789 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M magnesium chloride, 0.1 M imidazole buffer, 35% MPD, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.13→35.9 Å / Num. all: 115778 / Num. obs: 115778 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.096 / Χ2: 1.608 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.13-2.174.10.7551.9557341.34899.1
2.17-2.214.70.63457291.40898.8
2.21-2.255.20.57157301.51598.5
2.25-2.295.50.55457751.60798.5
2.29-2.345.50.43956491.64698.3
2.34-2.45.50.40857731.66898.2
2.4-2.465.60.3856901.64998.4
2.46-2.535.60.32957631.68498.2
2.53-2.65.60.27656801.70497.9
2.6-2.685.70.23457001.76698
2.68-2.785.70.20357241.73297.9
2.78-2.895.80.17757361.77198
2.89-3.025.90.14957411.75297.7
3.02-3.1860.12257341.72898.1
3.18-3.386.10.09758341.68899.2
3.38-3.646.20.08258741.59199.7
3.64-4.016.50.0758951.51199.9
4.01-4.596.90.06259311.484100
4.59-5.787.20.05759681.42299.9
5.78-506.90.04961181.49599.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PA6

2pa6


Resolution: 2.13→35.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 10.56 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.198 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 5674 5 %RANDOM
Rwork0.1761 ---
all0.1781 113627 --
obs0.1781 113627 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.79 Å2 / Biso mean: 36.2297 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å20 Å20 Å2
2---1.28 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.13→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12628 0 69 775 13472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213273
X-RAY DIFFRACTIONr_bond_other_d0.0010.028962
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.97518007
X-RAY DIFFRACTIONr_angle_other_deg0.973322010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07751780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72625.192624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.138152386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2881584
X-RAY DIFFRACTIONr_chiral_restr0.0920.22042
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022579
X-RAY DIFFRACTIONr_mcbond_it0.7881.58385
X-RAY DIFFRACTIONr_mcbond_other0.2061.53483
X-RAY DIFFRACTIONr_mcangle_it1.393213449
X-RAY DIFFRACTIONr_scbond_it2.3334888
X-RAY DIFFRACTIONr_scangle_it3.7014.54495
LS refinement shellResolution: 2.127→2.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 368 -
Rwork0.258 7368 -
all-7736 -
obs-7736 90 %
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)
10.4225-0.0352-0.14040.75130.11790.6356-0.03810.00690.00640.17170.03220.02470.15670.02340.00590.0785-0.01150.01240.06010.00740.026935.492-29.464732.7327
20.5871-0.09930.10191.01840.08080.5026-0.0393-0.0458-0.00910.27970.03280.1337-0.0224-0.0930.00650.1035-0.01150.05770.0877-0.00260.048326.8334-0.075244.1682
30.47740.0722-0.1340.7243-0.00360.72780.02880.02340.00030.1618-0.01170.0571-0.13680.0267-0.01710.0706-0.00950.03510.0582-0.00660.04635.528732.806929.4019
40.67070.0064-0.10090.8334-0.1210.8810.0608-0.00050.021-0.0053-0.01960.1447-0.2085-0.0742-0.04120.0680.03210.02720.0521-0.00330.073126.506744.19920.1239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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