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- PDB-4dg5: Crystal structure of staphylococcal Phosphoglycerate kinase -

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Basic information

Entry
Database: PDB / ID: 4dg5
TitleCrystal structure of staphylococcal Phosphoglycerate kinase
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / Bi-lobal protein / ATP Synthesis / phosphorylation / cytosol
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / 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
Phosphoglycerate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRoychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K.
CitationJournal: To be Published
Title: Structure based functional analysis of Staphylococcal Phosphoglycerate kinase
Authors: Roychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)43,4991
Polymers43,4991
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.137, 74.748, 58.665
Angle α, β, γ (deg.)90.000, 95.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoglycerate kinase


Mass: 43499.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: pgk, SAR0829 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q6GIL7, phosphoglycerate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.26 Å3/Da / Density % sol: 45.66 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.15M Calcium chloride dihydrate, 0.1M HEPES-Na, 20% (w/v)Polyethylene glycol 2000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2010 / Details: Varimax mirror
RadiationMonochromator: Varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→58.373 Å / Num. all: 16871 / Num. obs: 16871 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.094 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.423.60.2750.2353.2855524010.1430.2750.2355.295.9
2.42-2.573.70.2530.2163.4844323030.130.2530.2165.996.6
2.57-2.753.70.1950.1684.4806721590.10.1950.1687.497.3
2.75-2.973.80.1490.1285.7771420420.0760.1490.1289.597.8
2.97-3.253.80.1070.0927.9717918870.0540.1070.09212.697.8
3.25-3.643.80.0860.0749.6653117130.0440.0860.07416.298.9
3.64-4.23.80.0730.06311.4578215220.0370.0730.0632098.7
4.2-5.143.80.0670.05812.1489812920.0340.0670.05821.699.1
5.14-7.273.80.0780.06710.2381810110.040.0780.06717.499.7
7.27-19.4583.70.0540.04613.519765410.0280.0540.04624.994.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å19.46 Å
Translation4 Å19.46 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHP

1php


Resolution: 2.3→58.37 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.842 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.015 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 850 5 %RANDOM
Rwork0.1724 ---
obs0.1769 16852 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 15.703 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-0.42 Å2
2--0.6 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→58.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 0 260 3245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223047
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9774117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58826.504123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14115562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.866156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212230
X-RAY DIFFRACTIONr_mcbond_it0.7591.51957
X-RAY DIFFRACTIONr_mcangle_it1.41623150
X-RAY DIFFRACTIONr_scbond_it2.51531090
X-RAY DIFFRACTIONr_scangle_it4.1794.5964
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 52 -
Rwork0.169 1149 -
all-1201 -
obs--94.72 %
Refinement TLS params.Method: refined / Origin x: -3.9813 Å / Origin y: 8.927 Å / Origin z: -23.8766 Å
111213212223313233
T0.0141 Å20.0049 Å20.0159 Å2-0.0039 Å20.0086 Å2--0.0273 Å2
L0.6187 °20.184 °20.4823 °2-0.3317 °20.2049 °2--0.8203 °2
S0.0009 Å °-0.0326 Å °-0.0435 Å °0.0359 Å °0.0096 Å °0.0247 Å °-0.0096 Å °-0.0258 Å °-0.0106 Å °

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