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- PDB-3kkk: Y92C catalytic residue mutant of Phosphoglycerate Mutase from Pla... -

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Basic information

Entry
Database: PDB / ID: 3kkk
TitleY92C catalytic residue mutant of Phosphoglycerate Mutase from Plasmodium falciparum
ComponentsPhosphoglycerate mutase
KeywordsISOMERASE / PGAM / glycolysis / malaria / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / Neutrophil degranulation / glycolytic process / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate mutase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: To be Published
Title: Structure of a phosphoglycerate mutase from Plasmodium falciparum
Authors: Larson, E.T. / Caruthers, J.M. / Zhang, L. / Hol, W.G.J. / Merritt, E.A.
History
DepositionNov 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 22, 2025Group: Structure summary / Category: audit_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate mutase
B: Phosphoglycerate mutase
C: Phosphoglycerate mutase
D: Phosphoglycerate mutase


Theoretical massNumber of molelcules
Total (without water)119,1494
Polymers119,1494
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-25 kcal/mol
Surface area40420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.062, 76.120, 101.680
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoglycerate mutase


Mass: 29787.223 Da / Num. of mol.: 4 / Mutation: Y92C
Source method: isolated from a genetically manipulated source
Details: N-terminal 6xHis tag added during cloning, Y92C mutation confirmed from plasmid sequence
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF11_0208 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IIG6, EC: 5.4.2.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 35% PEG 1000, 0.1 M HEPES pH 7.2, 0.1 M KSCN, 5 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91837 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 20, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 64085 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.045 / Net I/σ(I): 10.5
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.22 / Num. unique all: 6390 / Χ2: 1.005 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.74 Å32.5 Å
Translation2.74 Å32.5 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xq9

1xq9


Resolution: 2.08→31.46 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.107 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3209 5 %RANDOM
Rwork0.196 ---
obs0.198 64066 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.19 Å2 / Biso mean: 26.78 Å2 / Biso min: 2.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.11 Å2
2---0.07 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.08→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7485 0 0 244 7729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227746
X-RAY DIFFRACTIONr_bond_other_d0.0010.025314
X-RAY DIFFRACTIONr_angle_refined_deg0.931.9610539
X-RAY DIFFRACTIONr_angle_other_deg0.791313032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44124.429350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.022151388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1361537
X-RAY DIFFRACTIONr_chiral_restr0.0580.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021490
X-RAY DIFFRACTIONr_mcbond_it1.05644632
X-RAY DIFFRACTIONr_mcbond_other0.28441835
X-RAY DIFFRACTIONr_mcangle_it1.7567553
X-RAY DIFFRACTIONr_scbond_it2.08463114
X-RAY DIFFRACTIONr_scangle_it3.164102981
LS refinement shellResolution: 2.08→2.131 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 187 -
Rwork0.328 4270 -
all-4457 -
obs--94.59 %
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)
14.44530.3275-0.92821.4412-0.42713.0399-0.00770.2098-0.4917-0.24110.06430.17750.2737-0.0999-0.05650.1765-0.0056-0.01080.0211-0.04280.207819.3922-0.109615.7028
24.7486-0.1992-0.14541.57420.1811.8833-0.0576-0.3927-0.36030.19180.0361-0.08810.10380.02150.02150.15660.02850.0220.13410.06890.125945.94143.248937.8425
33.7214-0.08130.50322.07090.34564.4729-0.124-0.21230.55350.0882-0.0522-0.2363-0.39350.58140.17620.2179-0.051-0.03070.11790.01050.226246.582335.226530.6821
44.03170.6681.3512.61830.67874.031-0.19150.11910.4844-0.174-0.08190.4815-0.4354-0.51820.27350.21160.0872-0.05080.1028-0.03390.264314.699232.408217.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 231
2X-RAY DIFFRACTION2B1 - 231
3X-RAY DIFFRACTION3C2 - 231
4X-RAY DIFFRACTION4D2 - 231

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