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- PDB-1ltk: CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM PLASMODIUM FALC... -

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Basic information

Entry
Database: PDB / ID: 1ltk
TitleCRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM PLASMODIUM FALCIPARUM, IN THE OPEN CONFORMATION
ComponentsPHOSPHOGLYCERATE KINASE
KeywordsTRANSFERASE / PGK / PHOSPHOGLYCERATE KINASE / GLYCOLYSIS / GLYCEROL / OPEN CONFORMATION / ADP COMPLEX / SELENOMETHIONINE
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsChattopadhyay, D. / Pal, B. / Smith, C.D.
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM PLASMODIUM FALCIPARUM
Authors: Chattopadhyay, D. / Pal, B. / Smith, C.D.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 30, 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 / 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 / _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_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_comp_id / _struct_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: PHOSPHOGLYCERATE KINASE
B: PHOSPHOGLYCERATE KINASE
C: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,49010
Polymers141,0683
Non-polymers1,4227
Water1,29772
1
A: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5584
Polymers47,0231
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4663
Polymers47,0231
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4663
Polymers47,0231
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.030, 147.610, 206.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PHOSPHOGLYCERATE KINASE


Mass: 47022.602 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PGK / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P27362, phosphoglycerate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.2 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9537, 0.9792, 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2001
RadiationMonochromator: DOUBLE CRYSTAL SILICON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97921
30.97931
ReflectionResolution: 3→50 Å / Num. all: 34732 / Num. obs: 36637 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rsym value: 0.058 / Net I/σ(I): 11.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.2 % / Rsym value: 0.208 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEVERSION 1.18phasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 5233465.22 / Data cutoff high rms absF: 5233465.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3454 9.9 %RANDOM
Rwork0.208 ---
all0.2845 34732 --
obs0.2845 34732 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.8077 Å2 / ksol: 0.327644 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2--2.01 Å20 Å2
3---0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9643 0 90 72 9805
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 503 9.7 %
Rwork0.391 4689 -
obs-5192 85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2AMP.PARAMAMP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMGOL.TOP
X-RAY DIFFRACTION4ION.PARAMWATER.TOP
X-RAY DIFFRACTION5GOL.PARAMION.TOP

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