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- PDB-3igz: Crystal structures of Leishmania mexicana phosphoglycerate mutase... -

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Basic information

Entry
Database: PDB / ID: 3igz
TitleCrystal structures of Leishmania mexicana phosphoglycerate mutase at low cobalt concentration
ComponentsCofactor-independent phosphoglycerate mutase
KeywordsISOMERASE / glycolysis / mutase / cobalt
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 / cytoplasm
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
2-PHOSPHOGLYCERIC ACID / 3-PHOSPHOGLYCERIC ACID / : / phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNowicki, M.W. / Kuaprasert, B. / McNae, I.W. / Morgan, H.P. / Harding, M.M. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass
Authors: Nowicki, M.W. / Kuaprasert, B. / McNae, I.W. / Morgan, H.P. / Harding, M.M. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionJul 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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_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_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.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_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

Downloads & links

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Assembly

Deposited unit
B: Cofactor-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3886
Polymers61,8751
Non-polymers5135
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.464, 72.267, 129.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Cofactor-independent phosphoglycerate mutase


Mass: 61875.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86N96, EC: 5.4.2.1

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Non-polymers , 5 types, 636 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID / 2-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.: 631 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRESIDUE 3PG 564 AND 2PG 565 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 47.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.3
Details: 80mM Ammonium acetate, 40mM trisodium citrate pH 6.0, 24%(w/v) PEG4000, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→19.965 Å / Num. obs: 48626 / % possible obs: 98.55 % / Observed criterion σ(F): 1.34
Reflection shellResolution: 1.9→1.939 Å / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.965 Å / SU ML: 0.2 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 2338 5.05 %
Rwork0.156 --
obs0.1574 46288 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.863 Å2 / ksol: 0.373 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→19.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 25 631 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144375
X-RAY DIFFRACTIONf_angle_d1.3845929
X-RAY DIFFRACTIONf_dihedral_angle_d17.7191605
X-RAY DIFFRACTIONf_chiral_restr0.099641
X-RAY DIFFRACTIONf_plane_restr0.005791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93880.25931230.1832247296
1.9388-1.98090.17321420.1767248397
1.9809-2.02690.19421390.1662250696
2.0269-2.07760.2071510.1683250698
2.0776-2.13370.19361450.1602254599
2.1337-2.19640.19031160.1598256798
2.1964-2.26720.16721290.1546258299
2.2672-2.34810.20041390.1589255699
2.3481-2.4420.18391300.1628258399
2.442-2.55290.18761180.1575261299
2.5529-2.68720.2021590.1561260099
2.6872-2.85510.17641420.1621257799
2.8551-3.07480.19241360.16362618100
3.0748-3.38290.1961430.1563260899
3.3829-3.86930.16211150.13292678100
3.8693-4.86320.12641580.121267199
4.8632-19.96570.17651530.1577278699

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