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- PDB-3gw8: Crystal structure of phosphoglyceromutase from Burkholderia pseud... -

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Basic information

Entry
Database: PDB / ID: 3gw8
TitleCrystal structure of phosphoglyceromutase from Burkholderia pseudomallei with vanadate and glycerol
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / SSGCID / NIAID / deCODE / UWPPG / SBRI / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / glycolytic process / gluconeogenesis
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
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: 1.93 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 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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)59,33912
Polymers57,9182
Non-polymers1,42110
Water5,675315
1
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8637
Polymers28,9591
Non-polymers9056
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)29,4755
Polymers28,9591
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.175, 49.112, 62.590
Angle α, β, γ (deg.)106.420, 91.180, 107.610
Int Tables number1
Space group name H-MP1

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Components

#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 a non-cleavable N-terminal 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
#2: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 43.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Emerald Cryo Screen B-4, 100 mM MES pH 6.0, 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 FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 34058 / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Χ2: 1.666 / Net I/σ(I): 21.975
Reflection shellResolution: 1.93→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.89 / Num. unique all: 2972 / Χ2: 1.127 / % possible all: 80.4

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Phasing

PhasingMethod: molecular replacement

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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
Starting model: 3EZN

3ezn


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.859 / SU B: 3.495 / SU ML: 0.102 / SU R Cruickshank DPI: 0.192 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1696 5 %RANDOM
Rwork0.187 ---
obs0.189 34057 92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.82 Å2 / Biso mean: 22.537 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.31 Å2-0.28 Å2
2---0.38 Å20.17 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 82 315 4063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223879
X-RAY DIFFRACTIONr_bond_other_d0.0010.022664
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9775265
X-RAY DIFFRACTIONr_angle_other_deg0.83836461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77823.37181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78315617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0381533
X-RAY DIFFRACTIONr_chiral_restr0.0690.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
X-RAY DIFFRACTIONr_mcbond_it0.551.52320
X-RAY DIFFRACTIONr_mcbond_other0.1151.5928
X-RAY DIFFRACTIONr_mcangle_it1.01923742
X-RAY DIFFRACTIONr_scbond_it1.51131559
X-RAY DIFFRACTIONr_scangle_it2.5054.51523
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 92 -
Rwork0.26 2017 -
all-2109 -
obs--77.28 %

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