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- PDB-4fey: An X-ray Structure of a Putative Phosphogylcerate Kinase with Bou... -

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Basic information

Entry
Database: PDB / ID: 4fey
TitleAn X-ray Structure of a Putative Phosphogylcerate Kinase with Bound ADP from Francisella tularensis subsp. tularensis SCHU S4
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / phosphorylation / ATP binding / cytoplasm
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-5'-DIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: An X-ray Structure of a Putative Phosphogylcerate Kinase with Bound ADP from Francisella tularensis subsp. tularensis SCHU S4
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6852
Polymers42,2581
Non-polymers4271
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.616, 66.616, 206.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Phosphoglycerate kinase /


Mass: 42257.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_1367c, pgk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q5NF76, phosphoglycerate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG3350, 50mM ADA pH7,ADP 1mM, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2011 / Details: Be Lenses
RadiationMonochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 19816 / Num. obs: 19816 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 68.59 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 32.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.66 / Num. unique all: 984 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHASERphasing
PHENIXmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EHJ

4ehj


Resolution: 2.3→27.99 Å / Cor.coef. Fo:Fc: 0.9618 / Cor.coef. Fo:Fc free: 0.9407 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1013 5.12 %RANDOM
Rwork0.1932 ---
all0.1959 ---
obs0.1959 19788 --
Displacement parametersBiso mean: 82.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.0612 Å20 Å20 Å2
2---1.0612 Å20 Å2
3---2.1224 Å2
Refine analyzeLuzzati coordinate error obs: 0.496 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 27 117 3092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013032HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14103HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1429SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it3003HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_chiral_improper_torsion416SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3476SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3356 152 5.27 %
Rwork0.255 2734 -
all0.2591 2886 -
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)
16.33094.39396.271911.4653.2271.4615-0.0909-0.0310.7692-0.1242-0.0673-0.3039-0.4726-0.08980.1582-0.2186-0.45590.2236-0.1499-0.45350.60524.386189.2292-35.4951
23.2224-2.4557-1.84346.98170.77962.87670.20410.62811.143-1.54650.3988-0.364-0.8012-0.17-0.60290.0889-0.31320.2788-0.31710.1279-0.187813.125482.5935-48.314
305.75730.51754.8323-1.36683.73920.13170.3514-0.4093-0.35420.17660.4297-0.0053-0.2937-0.30830.283-0.38890.17750.1006-0.0348-0.38118.955563.1696-50.4746
46.30781.3952-3.50532.90170.59784.7542-0.01531.39031.0832-1.17860.2992-0.4868-0.4386-0.0872-0.28390.1712-0.31980.25670.13270.1679-0.13616.711676.6005-53.6919
52.2946-1.59291.65370.04960.69832.6319-0.01090.1496-0.1629-0.11730.0748-0.42450.37020.38-0.0639-0.1226-0.08280.13760.0188-0.2001-0.0422.770665.1128-39.6819
67.0082-3.5899-3.25442.52721.6863.4397-0.0385-0.37111.24-0.28550.5441-0.9285-0.43920.6774-0.5055-0.1402-0.24290.0746-0.0574-0.18040.11117.826479.2392-36.0791
73.164-2.3453-0.4975.31610.50092.9093-0.5717-0.69070.06190.70170.47470.2407-0.0135-0.19760.097-0.07530.1192-0.00330.0228-0.0692-0.2802-7.998378.7079-18.7336
83.6793-1.4270.71082.732-1.61561.3234-0.1464-0.8669-0.31571.28450.1257-0.0351-0.4985-0.22030.02070.32410.16720.13340.25970.0724-0.2948-9.015971.8544-11.8986
95.25240.23390.10195.76271.07082.388-0.418-0.13420.7144-0.230.19210.8826-0.4387-0.51550.2259-0.15320.0875-0.1461-0.1187-0.0407-0.1327-13.586684.7656-26.8941
1000.51264.93200.488700.0499-0.53180.1832-0.02180.2377-0.651-0.20.0244-0.2876-0.1891-0.0865-0.0090.084-0.29250.194121.492578.5103-28.0729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 12}A1 - 12
2X-RAY DIFFRACTION2{A|13 - 61}A13 - 61
3X-RAY DIFFRACTION3{A|62 - 71}A62 - 71
4X-RAY DIFFRACTION4{A|72 - 118}A72 - 118
5X-RAY DIFFRACTION5{A|119 - 128}A119 - 128
6X-RAY DIFFRACTION6{A|129 - 176}A129 - 176
7X-RAY DIFFRACTION7{A|177 - 234}A177 - 234
8X-RAY DIFFRACTION8{A|235 - 251}A235 - 251
9X-RAY DIFFRACTION9{A|252 - 378}A252 - 378
10X-RAY DIFFRACTION10{A|379 - 392}A379 - 392

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