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

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Basic information

Entry
Database: PDB / ID: 3ezn
TitleCrystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / SSGCID / PHOSPHOGLYCEROMUTASE / BURKHOLDERIA PSEUDOMALLEI / 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
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Sep 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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

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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)58,6956
Polymers57,9182
Non-polymers7774
Water6,575365
1
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3473
Polymers28,9591
Non-polymers3882
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)29,3473
Polymers28,9591
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.940, 49.080, 62.110
Angle α, β, γ (deg.)107.11, 91.19, 107.81
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PG4 / End label comp-ID: PG4 / Refine code: 6 / Auth seq-ID: 1 - 250 / Label seq-ID: 9

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - E

NCS ensembles : (Details: A B)

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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
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1719B / Gene: gpmA, BURPS1710b_0662 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JWH7, EC: 5.4.2.1
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EMERALD CRYO B-4: 100MM MES PH 6.0, 5% PEG 1000, 10% GLYCEROL, 30% PEG 600, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: SATURN 944 / Detector: CCD / Date: Sep 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 26261 / Num. obs: 26261 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 22.93 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 25.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1736 / Rsym value: 0.137 / % possible all: 83.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0046refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x19 modified with ccp4 chainsaw

1x19


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.047 / SU ML: 0.11 / Isotropic thermal model: isotrpoic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1315 5 %RANDOM
Rwork0.15 ---
all0.152 26261 --
obs0.152 26261 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.36 Å2-0.4 Å2
2---0.15 Å20.18 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 37 365 4105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223850
X-RAY DIFFRACTIONr_bond_other_d0.0010.022627
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9675237
X-RAY DIFFRACTIONr_angle_other_deg0.97936370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7215469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45223.278180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35115615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6511533
X-RAY DIFFRACTIONr_chiral_restr0.1060.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
X-RAY DIFFRACTIONr_mcbond_it0.961.52338
X-RAY DIFFRACTIONr_mcbond_other0.2751.5937
X-RAY DIFFRACTIONr_mcangle_it1.6923763
X-RAY DIFFRACTIONr_scbond_it2.73731512
X-RAY DIFFRACTIONr_scangle_it4.294.51472
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3028 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.45
loose thermal2.2510
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 74 -
Rwork0.147 1655 -
obs--83.25 %

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