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- PDB-3fdz: Crystal structure of phosphoglyceromutase from burkholderia pseud... -

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Basic information

Entry
Database: PDB / ID: 3fdz
TitleCrystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b with bound 2,3-diphosphoglyceric acid and 3-phosphoglyceric acid
Components(2,3-bisphosphoglycerate-dependent phosphoglycerate ...) x 2
KeywordsISOMERASE / SSGCID / Phosphoglyceromutase / Burkholderia pseudomallei / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process
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
3-PHOSPHOGLYCERIC ACID / (2R)-2,3-diphosphoglyceric acid / DI(HYDROXYETHYL)ETHER / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase.
Authors: Davies, D.R. / Staker, B.L. / Abendroth, J.A. / Edwards, T.E. / Hartley, R. / Leonard, J. / Kim, H. / Rychel, A.L. / Hewitt, S.N. / Myler, P.J. / Stewart, L.J.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Jul 20, 2016Group: Non-polymer description
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6616
Polymers57,9972
Non-polymers6644
Water4,017223
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint4 kcal/mol
Surface area18590 Å2
MethodPISA
2
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3313
Polymers28,9591
Non-polymers3722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3313
Polymers28,9591
Non-polymers3722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.390, 48.480, 62.090
Angle α, β, γ (deg.)106.03, 91.54, 107.50
Int Tables number1
Space group name H-MP1
DetailsThe asymmetric unit contains two biological units

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Components

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2,3-bisphosphoglycerate-dependent phosphoglycerate ... , 2 types, 2 molecules AB

#1: Protein 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / Phosphoglyceromutase / PGAM / BPG-dependent PGAM / dPGM


Mass: 28958.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1719B / Gene: BURPS1710b_0662, gpmA / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q3JWH7, EC: 5.4.2.1
#2: Protein 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / Phosphoglyceromutase / PGAM / BPG-dependent PGAM / dPGM


Mass: 29037.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1719B / Gene: BURPS1710b_0662, gpmA / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q3JWH7, EC: 5.4.2.1

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Non-polymers , 4 types, 227 molecules

#3: Chemical ChemComp-DG2 / (2R)-2,3-diphosphoglyceric acid / 2,3-Bisphosphoglyceric acid / 2,3-bisphosphoglycerate / 2,3-BPG / 2,3-diphosphoglyceric acid / 2,3-diphosphoglycerate / 2,3-DPG / (2~{R})-2,3-diphosphonooxypropanoic acid / 2,3-Bisphosphoglyceric acid


Mass: 266.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O10P2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 289 K / pH: 6
Details: 30% PEG 600, 5% PEG 1000, 10% GLYCEROL, 100 MM MES PH 6.0, CRYSTALS SOAKED OVERNIGHT WITH 20 MM 3-PHOSPHOGLYCERIC ACID, VAPOR DIFFUSION, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: SATURN / Detector: CCD / Date: Sep 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. obs: 20934 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.18 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.43
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.6 / % possible all: 90.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0053refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.75 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.03 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.418 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1066 5.1 %RANDOM
Rwork0.183 ---
obs0.187 20934 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.12 Å2-1.14 Å2
2---0.45 Å2-0.05 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 40 223 3931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9745175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44523.39177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59315610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9041532
X-RAY DIFFRACTIONr_chiral_restr0.0910.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212905
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5851.52291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05923693
X-RAY DIFFRACTIONr_scbond_it1.92331505
X-RAY DIFFRACTIONr_scangle_it3.0134.51482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 82 -
Rwork0.252 1440 -
obs--90.87 %

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