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- PDB-4drs: Crystal structure of Cryptosporidium parvum pyruvate kinase -

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Basic information

Entry
Database: PDB / ID: 4drs
TitleCrystal structure of Cryptosporidium parvum pyruvate kinase
ComponentsPyruvate kinase
KeywordsTRANSFERASE / pyruvate / kinase / glycolysis / cryptosporidium / allosteric enzyme
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCook, W.J. / Chattopadhyay, D.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure of Cryptosporidium parvum pyruvate kinase.
Authors: Cook, W.J. / Senkovich, O. / Aleem, K. / Chattopadhyay, D.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,08716
Polymers112,9802
Non-polymers1,10714
Water2,684149
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,17532
Polymers225,9614
Non-polymers2,21428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area18270 Å2
ΔGint-225 kcal/mol
Surface area74480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.895, 136.941, 77.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 6 / Label seq-ID: 23

Dom-IDAuth asym-IDLabel asym-IDAuth seq-ID
1AA - Q23 - 740
2BB - R23 - 741

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Components

#1: Protein Pyruvate kinase /


Mass: 56490.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd1_2040 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CSM7, pyruvate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.4-0.8 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 47349 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1
Reflection shellResolution: 2.5→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PKL

1pkl


Resolution: 2.5→49.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.579 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24949 2344 5 %RANDOM
Rwork0.2134 ---
obs0.21523 45005 97.78 %-
all-37504 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 68 149 7505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.98210060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1285964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71825.255274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.634151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9541534
X-RAY DIFFRACTIONr_chiral_restr0.060.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021292
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_it0.6511.54872
X-RAY DIFFRACTIONr_mcbond_other0.0551.51982
X-RAY DIFFRACTIONr_mcangle_it1.20527904
X-RAY DIFFRACTIONr_scbond_it1.02132604
X-RAY DIFFRACTIONr_scangle_it1.8164.52208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 6227 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.235
Bloose thermal1.9410
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 148 -
Rwork0.273 3101 -
obs--98.72 %
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)
12.67561.70540.79531.09740.51050.2397-0.33970.48370.4007-0.16760.25860.2336-0.07930.15710.08110.1668-0.0909-0.06490.34660.10280.174411.286-19.819-29.798
21.7685-0.1582-1.03830.09170.18661.8448-0.03720.0147-0.1335-0.0127-0.0054-0.06760.16080.01170.04260.16720.02780.03140.1467-0.00490.095629.39-36.653-14.774
34.1533-0.1555-2.75563.34873.3197.0184-0.77930.3631-0.49850.1487-0.02160.19680.5478-0.27230.80090.1678-0.05990.11090.1733-0.05540.15169.322-52.775.077
41.6006-0.29870.49680.2516-0.31170.8244-0.0455-0.1804-0.04410.05220.0223-0.00860.0227-0.0880.02320.12610.0175-0.00710.20580.00320.059819.474-27.39-0.421
513.5917-5.98326.15933.5319-4.79897.64720.702-0.5528-0.9085-0.38130.30310.66720.5019-0.297-1.00510.3729-0.06830.04520.05170.0140.19229.289-38.987-22.051
60.66671.0812-0.19372.40380.46971.070.0070.13370.02490.07830.0507-0.00810.0468-0.1407-0.05770.08480.0242-0.02950.2404-0.00280.074314.62-19.727-19.118
71.3067-0.8080.24222.257-1.35581.34470.04660.098-0.004-0.1754-0.1758-0.23820.07340.08690.12920.12220.01130.02220.16080.0010.104629.764-10.81-22.488
81.5887-0.2707-0.39410.08160.04050.1224-0.0989-0.31060.13980.00510.1320.01720.06750.0279-0.03310.21290.03070.00770.251-0.01970.1156-10.328-28.693-12.774
90.60430.1192-0.90460.8273-0.30182.1377-0.0006-0.0506-0.1273-0.03650.00770.05150.2115-0.0004-0.00710.144-0.028-0.00240.19290.00350.1115-22.976-41.072-23.853
107.311-1.2929-3.61581.2597-1.26615.5569-1.3135-1.2354-1.07150.14870.20620.01840.95910.69381.10730.33340.23090.35370.31070.20290.43330.585-53.491-43.697
111.0510.43550.47230.42470.0830.6517-0.06220.1824-0.0031-0.09350.04520.030.05340.12660.0170.128-0.0279-0.01230.2445-0.01740.0541-13.533-30.288-38.218
1227.25767.76124.338610.4899-7.12739.13950.89761.764-3.5441.25891.37880.4075-0.7734-0.8742-2.27640.35120.17860.10340.2761-0.04560.7505-3.477-41.101-17.547
130.9788-1.1702-0.00821.8665-0.64510.92810.062-0.06170.0247-0.1173-0.0617-0.0140.05140.1613-0.00030.0832-0.0521-0.02480.2325-0.02270.0757-10.01-22.723-18.705
140.81260.1454-0.09071.77930.34980.34820.05140.0483-0.04980.1042-0.03230.1954-0.04450.0026-0.0190.1184-0.02580.00920.1499-0.01740.1263-27.59-16.125-16.373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 48
2X-RAY DIFFRACTION2A49 - 113
3X-RAY DIFFRACTION3A114 - 206
4X-RAY DIFFRACTION4A207 - 327
5X-RAY DIFFRACTION5A328 - 344
6X-RAY DIFFRACTION6A345 - 418
7X-RAY DIFFRACTION7A419 - 526
8X-RAY DIFFRACTION8B23 - 57
9X-RAY DIFFRACTION9B58 - 112
10X-RAY DIFFRACTION10B113 - 204
11X-RAY DIFFRACTION11B205 - 326
12X-RAY DIFFRACTION12B327 - 340
13X-RAY DIFFRACTION13B341 - 419
14X-RAY DIFFRACTION14B420 - 526

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