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- PDB-4nwj: Crystal structure of phosphopglycerate mutase from Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 4nwj
TitleCrystal structure of phosphopglycerate mutase from Staphylococcus aureus in 3-phosphoglyceric acid bound form.
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / glycolytic enzyme / cytosol
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glucose catabolic process / glycolytic process / manganese ion binding / carbohydrate metabolic process / cytosol
Similarity search - Function
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain / BPG-independent phosphoglycerate mutase, domain B / Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent / BPG-independent PGAM, N-terminal / BPG-independent phosphoglycerate mutase, domain B superfamily / BPG-independent PGAM N-terminus (iPGM_N) / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A ...2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain / BPG-independent phosphoglycerate mutase, domain B / Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent / BPG-independent PGAM, N-terminal / BPG-independent phosphoglycerate mutase, domain B superfamily / BPG-independent PGAM N-terminus (iPGM_N) / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / : / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsRoychowdhury, A. / Bose, M. / Kundu, A. / Gujar, A. / Das, A.K.
CitationJournal: Febs J. / Year: 2015
Title: Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism
Authors: Roychowdhury, A. / Kundu, A. / Bose, M. / Gujar, A. / Mukherjee, S. / Das, A.K.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Nov 8, 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_ref_seq_dif / 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_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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,7574
Polymers57,4611
Non-polymers2963
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.637, 82.841, 89.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / BPG-independent PGAM / Phosphoglyceromutase / iPGM


Mass: 57460.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC8325 / Gene: gpmI, SAOUHSC_00798 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q2G029, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.2M NaCl, Bis-Tris, 25%(w/v) PEG3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2013 / Details: Varimax (osmic mirror)
RadiationMonochromator: varimax (osmic mirror) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→60.684 Å / Num. all: 35948 / Num. obs: 35948 / % possible obs: 96.9 % / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.01-2.126.60.4461.70.446187.6
2.12-2.247.40.3342.30.334197.1
2.24-2.47.40.2433.20.243197.7
2.4-2.597.40.1784.30.178198.3
2.59-2.847.40.12960.129198.5
2.84-3.177.40.0829.40.082199.3
3.17-3.667.40.0515.40.05199.5
3.66-4.497.30.03322.50.033199.8
4.49-6.357.20.0323.50.031100
6.35-19.6266.80.02428.20.024196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MY4

4my4


Resolution: 2.01→19.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.567 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21667 1798 5 %RANDOM
Rwork0.16414 ---
obs0.16682 34105 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å2-0 Å2
2--0.49 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.01→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 13 296 4263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194063
X-RAY DIFFRACTIONr_bond_other_d0.0010.023780
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9595508
X-RAY DIFFRACTIONr_angle_other_deg1.01538706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.57825.472212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56415684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1491519
X-RAY DIFFRACTIONr_chiral_restr0.1720.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 109 -
Rwork0.198 2028 -
obs--78.28 %

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