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- PDB-3gp5: Crystal structure of phosphoglyceromutase from Burkholderia pseud... -

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Basic information

Entry
Database: PDB / ID: 3gp5
TitleCrystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 3-phosphoglyceric acid and vanadate
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / phosphoglyceromutase / deCODE / UWPPG. SBRI / NIAID / SSGCID / 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 / Chem-PG6 / VANADATE ION / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1749
Polymers57,9182
Non-polymers1,2577
Water4,053225
1
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5264
Polymers28,9591
Non-polymers5673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6485
Polymers28,9591
Non-polymers6894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.749, 48.983, 62.960
Angle α, β, γ (deg.)105.460, 91.150, 107.420
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 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.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal non-cleavable hexahis tag
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gpmA, BPSL0443 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63XU7, UniProt: Q3JWH7*PLUS, EC: 5.4.2.1

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Non-polymers , 5 types, 232 molecules

#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Emerald Cryo B-4, 100MM MES PH 7.5, 5% PEG 1000, 10% GLYCEROL, 30% PEG 600, 11.7 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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 SATURN 944 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 21960 / % possible obs: 94.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.068 / Χ2: 1.318 / Net I/σ(I): 13.141
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.452 / Num. unique all: 1899 / Χ2: 1.178 / % possible all: 82.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.36 Å33.92 Å
Translation2.36 Å33.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.838 / SU B: 5.868 / SU ML: 0.148 / SU R Cruickshank DPI: 0.377 / SU Rfree: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1121 5.1 %RANDOM
Rwork0.171 ---
obs0.174 21960 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.02 Å2 / Biso mean: 22.897 Å2 / Biso min: 3.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.17 Å2-1.05 Å2
2---0.8 Å20.5 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 73 225 4069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223920
X-RAY DIFFRACTIONr_bond_other_d0.0010.022657
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9755327
X-RAY DIFFRACTIONr_angle_other_deg0.97336453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87723.408179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81115621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7281532
X-RAY DIFFRACTIONr_chiral_restr0.1210.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
X-RAY DIFFRACTIONr_mcbond_it0.8181.52375
X-RAY DIFFRACTIONr_mcbond_other0.2111.5953
X-RAY DIFFRACTIONr_mcangle_it1.45323817
X-RAY DIFFRACTIONr_scbond_it2.431545
X-RAY DIFFRACTIONr_scangle_it3.6944.51510
LS refinement shellResolution: 2.246→2.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 77 -
Rwork0.215 1210 -
all-1287 -
obs--74.78 %

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